Started by upstream project "Trigger" build number 719 originally caused by: Started by timer Running as SYSTEM Building remotely on testintegration (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-test-integration [OMERO-test-integration] $ /bin/bash -xe /tmp/jenkins13266740465431495973.sh + rm -rf /home/omero/workspace/OMERO-test-integration/.venv3 + python3.11 -m venv /home/omero/workspace/OMERO-test-integration/.venv3 + source /home/omero/workspace/OMERO-test-integration/.venv3/bin/activate ++ deactivate nondestructive ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ '[' -n '' ']' ++ unset VIRTUAL_ENV ++ unset VIRTUAL_ENV_PROMPT ++ '[' '!' nondestructive = nondestructive ']' ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-test-integration/.venv3 ++ export VIRTUAL_ENV ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ PATH=/home/omero/workspace/OMERO-test-integration/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ export PATH ++ '[' -n '' ']' ++ '[' -z '' ']' ++ _OLD_VIRTUAL_PS1= ++ PS1='(.venv3) ' ++ export PS1 ++ VIRTUAL_ENV_PROMPT='(.venv3) ' ++ export VIRTUAL_ENV_PROMPT ++ hash -r + pip install -U pip setuptools Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1) Collecting pip Using cached pip-25.3-py3-none-any.whl (1.8 MB) Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (65.5.1) Collecting setuptools Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB) Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 65.5.1 Uninstalling setuptools-65.5.1: Successfully uninstalled setuptools-65.5.1 Attempting uninstall: pip Found existing installation: pip 22.3.1 Uninstalling pip-22.3.1: Successfully uninstalled pip-22.3.1 Successfully installed pip-25.3 setuptools-80.9.0 WARNING: There was an error checking the latest version of pip. + pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl Collecting zeroc-ice==3.6.5 Downloading https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl (37.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 11.4 MB/s 0:00:03 Installing collected packages: zeroc-ice Successfully installed zeroc-ice-3.6.5 + pip install markdown Collecting markdown Using cached markdown-3.10-py3-none-any.whl.metadata (5.1 kB) Using cached markdown-3.10-py3-none-any.whl (107 kB) Installing collected packages: markdown Successfully installed markdown-3.10 + pip install mox3 pytest pytest-django pytest-xdist pytest-mock Collecting mox3 Using cached mox3-1.1.0-py3-none-any.whl.metadata (3.2 kB) Collecting pytest Using cached pytest-9.0.2-py3-none-any.whl.metadata (7.6 kB) Collecting pytest-django Using cached pytest_django-4.11.1-py3-none-any.whl.metadata (8.3 kB) Collecting pytest-xdist Using cached pytest_xdist-3.8.0-py3-none-any.whl.metadata (3.0 kB) Collecting pytest-mock Using cached pytest_mock-3.15.1-py3-none-any.whl.metadata (3.9 kB) Collecting pbr!=2.1.0,>=2.0.0 (from mox3) Using cached pbr-7.0.3-py2.py3-none-any.whl.metadata (3.8 kB) Collecting fixtures>=3.0.0 (from mox3) Using cached fixtures-4.2.6-py3-none-any.whl.metadata (22 kB) Collecting iniconfig>=1.0.1 (from pytest) Using cached iniconfig-2.3.0-py3-none-any.whl.metadata (2.5 kB) Collecting packaging>=22 (from pytest) Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB) Collecting pluggy<2,>=1.5 (from pytest) Using cached pluggy-1.6.0-py3-none-any.whl.metadata (4.8 kB) Collecting pygments>=2.7.2 (from pytest) Using cached pygments-2.19.2-py3-none-any.whl.metadata (2.5 kB) Collecting execnet>=2.1 (from pytest-xdist) Using cached execnet-2.1.2-py3-none-any.whl.metadata (2.9 kB) Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from pbr!=2.1.0,>=2.0.0->mox3) (80.9.0) Using cached mox3-1.1.0-py3-none-any.whl (43 kB) Using cached pytest-9.0.2-py3-none-any.whl (374 kB) Using cached pluggy-1.6.0-py3-none-any.whl (20 kB) Using cached pytest_django-4.11.1-py3-none-any.whl (25 kB) Using cached pytest_xdist-3.8.0-py3-none-any.whl (46 kB) Using cached pytest_mock-3.15.1-py3-none-any.whl (10 kB) Using cached execnet-2.1.2-py3-none-any.whl (40 kB) Using cached fixtures-4.2.6-py3-none-any.whl (66 kB) Using cached iniconfig-2.3.0-py3-none-any.whl (7.5 kB) Using cached packaging-25.0-py3-none-any.whl (66 kB) Using cached pbr-7.0.3-py2.py3-none-any.whl (131 kB) Using cached pygments-2.19.2-py3-none-any.whl (1.2 MB) Installing collected packages: pygments, pluggy, pbr, packaging, iniconfig, fixtures, execnet, pytest, mox3, pytest-xdist, pytest-mock, pytest-django Successfully installed execnet-2.1.2 fixtures-4.2.6 iniconfig-2.3.0 mox3-1.1.0 packaging-25.0 pbr-7.0.3 pluggy-1.6.0 pygments-2.19.2 pytest-9.0.2 pytest-django-4.11.1 pytest-mock-3.15.1 pytest-xdist-3.8.0 + pip install tables Collecting tables Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB) Collecting numpy>=1.20.0 (from tables) Using cached numpy-2.3.5-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB) Collecting numexpr>=2.6.2 (from tables) Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB) Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from tables) (25.0) Collecting py-cpuinfo (from tables) Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes) Collecting blosc2>=2.3.0 (from tables) Using cached blosc2-3.12.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.1 kB) Collecting typing-extensions>=4.4.0 (from tables) Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB) Collecting ndindex (from blosc2>=2.3.0->tables) Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB) Collecting msgpack (from blosc2>=2.3.0->tables) Using cached msgpack-1.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.1 kB) Collecting platformdirs (from blosc2>=2.3.0->tables) Using cached platformdirs-4.5.1-py3-none-any.whl.metadata (12 kB) Collecting requests (from blosc2>=2.3.0->tables) Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB) Collecting charset_normalizer<4,>=2 (from requests->blosc2>=2.3.0->tables) Using cached charset_normalizer-3.4.4-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (37 kB) Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables) Using cached idna-3.11-py3-none-any.whl.metadata (8.4 kB) Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables) Downloading urllib3-2.6.1-py3-none-any.whl.metadata (6.6 kB) Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables) Using cached certifi-2025.11.12-py3-none-any.whl.metadata (2.5 kB) Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB) Using cached blosc2-3.12.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.5 MB) Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (442 kB) Using cached numpy-2.3.5-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB) Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB) Using cached msgpack-1.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (426 kB) Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB) Using cached platformdirs-4.5.1-py3-none-any.whl (18 kB) Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB) Using cached requests-2.32.5-py3-none-any.whl (64 kB) Using cached charset_normalizer-3.4.4-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (151 kB) Using cached idna-3.11-py3-none-any.whl (71 kB) Downloading urllib3-2.6.1-py3-none-any.whl (131 kB) Using cached certifi-2025.11.12-py3-none-any.whl (159 kB) Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, numpy, ndindex, msgpack, idna, charset_normalizer, certifi, requests, numexpr, blosc2, tables Successfully installed blosc2-3.12.2 certifi-2025.11.12 charset_normalizer-3.4.4 idna-3.11 msgpack-1.1.2 ndindex-1.10.1 numexpr-2.14.1 numpy-2.3.5 platformdirs-4.5.1 py-cpuinfo-9.0.0 requests-2.32.5 tables-3.10.2 typing-extensions-4.15.0 urllib3-2.6.1 + pip install jinja2 Collecting jinja2 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB) Collecting MarkupSafe>=2.0 (from jinja2) Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.7 kB) Using cached jinja2-3.1.6-py3-none-any.whl (134 kB) Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB) Installing collected packages: MarkupSafe, jinja2 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6 + pip install PyYAML Collecting PyYAML Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB) Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB) Installing collected packages: PyYAML Successfully installed PyYAML-6.0.3 + pip install omero-py omero-web Collecting omero-py Using cached omero_py-5.21.3-py3-none-any.whl.metadata (6.5 kB) Collecting omero-web Using cached omero_web-5.30.0-py3-none-any.whl.metadata (8.2 kB) Collecting appdirs (from omero-py) Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB) Collecting future (from omero-py) Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB) Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.3.5) Collecting Pillow>=10.0.0 (from omero-py) Using cached pillow-12.0.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.8 kB) Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py) (6.0.3) Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5) Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.5) Collecting portalocker (from omero-py) Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB) Collecting concurrent-log-handler>=0.9.20 (from omero-web) Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB) Collecting Django<5.3,>=4.2.25 (from omero-web) Using cached django-5.2.9-py3-none-any.whl.metadata (4.1 kB) Collecting django-pipeline (from omero-web) Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB) Collecting django-cors-headers==3.7.0 (from omero-web) Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB) Collecting whitenoise>=5.3.0 (from omero-web) Using cached whitenoise-6.11.0-py3-none-any.whl.metadata (3.7 kB) Collecting gunicorn>=19.3 (from omero-web) Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB) Collecting omero-marshal>=0.7.0 (from omero-web) Using cached omero_marshal-0.9.1-py3-none-any.whl.metadata (2.4 kB) Collecting pytz (from omero-web) Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB) Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web) (25.0) Collecting importlib-resources (from omero-web) Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB) Collecting asgiref>=3.8.1 (from Django<5.3,>=4.2.25->omero-web) Using cached asgiref-3.11.0-py3-none-any.whl.metadata (9.3 kB) Collecting sqlparse>=0.3.1 (from Django<5.3,>=4.2.25->omero-web) Using cached sqlparse-0.5.4-py3-none-any.whl.metadata (4.7 kB) Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web) (80.9.0) Collecting wheel (from django-pipeline->omero-web) Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB) Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.4) Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.11) Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2.6.1) Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.11.12) Using cached omero_py-5.21.3-py3-none-any.whl (2.8 MB) Using cached omero_web-5.30.0-py3-none-any.whl (2.8 MB) Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB) Using cached django-5.2.9-py3-none-any.whl (8.3 MB) Using cached asgiref-3.11.0-py3-none-any.whl (24 kB) Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB) Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB) Using cached omero_marshal-0.9.1-py3-none-any.whl (88 kB) Using cached pillow-12.0.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.0 MB) Using cached portalocker-3.2.0-py3-none-any.whl (22 kB) Using cached sqlparse-0.5.4-py3-none-any.whl (45 kB) Using cached whitenoise-6.11.0-py3-none-any.whl (20 kB) Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB) Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB) Using cached future-1.0.0-py3-none-any.whl (491 kB) Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB) Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB) Using cached wheel-0.45.1-py3-none-any.whl (72 kB) Installing collected packages: pytz, appdirs, whitenoise, wheel, sqlparse, portalocker, Pillow, omero-marshal, importlib-resources, gunicorn, future, asgiref, omero-py, django-pipeline, Django, concurrent-log-handler, django-cors-headers, omero-web Successfully installed Django-5.2.9 Pillow-12.0.0 appdirs-1.4.4 asgiref-3.11.0 concurrent-log-handler-0.9.28 django-cors-headers-3.7.0 django-pipeline-4.1.0 future-1.0.0 gunicorn-23.0.0 importlib-resources-6.5.2 omero-marshal-0.9.1 omero-py-5.21.3 omero-web-5.30.0 portalocker-3.2.0 pytz-2025.2 sqlparse-0.5.4 wheel-0.45.1 whitenoise-6.11.0 [OMERO-test-integration] $ /bin/bash -xe /tmp/jenkins903313560941728790.sh + source /home/settings.env ++ OMERO_DB_HOST=pg ++ OMERO_DB_USER=postgres ++ OMERO_DB_PASS= ++ OMERO_ROOT_PASS=omero ++ OMERO_DATA_DIR=/OMERO ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR + OMERO_DB_NAME=OMERO-test-integration + SRC=/home/omero/workspace/OMERO-test-integration/src + OMERO_DIST=/home/omero/workspace/OMERO-test-integration/src/dist + export OMERODIR=/home/omero/workspace/OMERO-test-integration/src/dist + OMERODIR=/home/omero/workspace/OMERO-test-integration/src/dist + '[' -e /home/omero/workspace/OMERO-test-integration/src/dist ']' + source /home/omero/workspace/OMERO-test-integration/.venv3/bin/activate ++ deactivate nondestructive ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ '[' -n '' ']' ++ unset VIRTUAL_ENV ++ unset VIRTUAL_ENV_PROMPT ++ '[' '!' nondestructive = nondestructive ']' ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-test-integration/.venv3 ++ export VIRTUAL_ENV ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ PATH=/home/omero/workspace/OMERO-test-integration/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ export PATH ++ '[' -n '' ']' ++ '[' -z '' ']' ++ _OLD_VIRTUAL_PS1= ++ PS1='(.venv3) ' ++ export PS1 ++ VIRTUAL_ENV_PROMPT='(.venv3) ' ++ export VIRTUAL_ENV_PROMPT ++ hash -r + omero admin stop Waiting on shutdown. Use CTRL-C to exit .+ deactivate + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']' + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin + export PATH + unset _OLD_VIRTUAL_PATH + '[' -n '' ']' + hash -r + '[' -n '' ']' + unset VIRTUAL_ENV + unset VIRTUAL_ENV_PROMPT + '[' '!' '' = nondestructive ']' + unset -f deactivate + sleep 5 + dropdb -f -h pg -U postgres OMERO-test-integration + rm -rf /home/omero/workspace/OMERO-test-integration/config /home/omero/workspace/OMERO-test-integration/data /home/omero/workspace/OMERO-test-integration/omero-blitz-5.8.4-SNAPSHOT-python.zip /home/omero/workspace/OMERO-test-integration/omero_dropbox-5.7.1.dev0.tar.gz /home/omero/workspace/OMERO-test-integration/omero_marshal-0.9.2.dev0.tar.gz /home/omero/workspace/OMERO-test-integration/omero_py-5.22.0.dev0.tar.gz /home/omero/workspace/OMERO-test-integration/omero_scripts-5.9.2.dev0.tar.gz /home/omero/workspace/OMERO-test-integration/omero_web-5.30.1.dev0.tar.gz /home/omero/workspace/OMERO-test-integration/src /home/omero/workspace/OMERO-test-integration/version.properties Copied 1 artifact from "OMERO-build" build number 589 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 586 Copied 2 artifacts from "OMERO-build-build" build number 620 [OMERO-test-integration] $ /bin/bash -xe /tmp/jenkins2040877485917999088.sh + source /home/settings.env ++ OMERO_DB_HOST=pg ++ OMERO_DB_USER=postgres ++ OMERO_DB_PASS= ++ OMERO_ROOT_PASS=omero ++ OMERO_DATA_DIR=/OMERO ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR + export ZIP_FILE=/home/omero/workspace/OMERO-test-integration/omero-blitz-VERSION-python.zip + ZIP_FILE=/home/omero/workspace/OMERO-test-integration/omero-blitz-VERSION-python.zip + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-test-integration/version.properties + VERSION_PROPERTIES=/home/omero/workspace/OMERO-test-integration/version.properties + OMERO_DB_NAME=OMERO-test-integration + OMERO_DATA_DIR=/home/omero/workspace/OMERO-test-integration/data + mkdir -p /home/omero/workspace/OMERO-test-integration/data + SRC=/home/omero/workspace/OMERO-test-integration/src ++ ls openmicroscopy-5.6.3-576-49aa459db9-ice36-b589.zip + ZIP_SRC=openmicroscopy-5.6.3-576-49aa459db9-ice36-b589.zip + unzip 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creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__3/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__3/OMERO3A__2.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__3/OMERO3__5.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__4/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__4/OMERO3A__3.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__4/OMERO3__5.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__5/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__5/OMERO3A__4.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__6/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__6/OMERO3A__5.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__7/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__7/OMERO3A__6.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__8/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__8/OMERO3A__6.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__9/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3A__9/OMERO3A__8.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3__4/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3__4/OMERO3__1.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3__5/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3__5/OMERO3__4.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3__6/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3__6/OMERO3__5.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3__7/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO3__7/OMERO3__6.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.1__0/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.1__0/OMERO4__0.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.2__0/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.2__0/OMERO4.1__0.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.2__0/t/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.3__0/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.3__0/OMERO4.2__0.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.4__0/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.4__0/OMERO4.1__0.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4.4__0/OMERO4.3__0.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4__0/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO4__0/OMERO3A__11.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.0__0/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.0__0/OMERO4.4__0.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.1__1/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.1__1/OMERO5.0__0.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.1__1/OMERO5.1__0.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.2__0/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.2__0/OMERO5.1__1.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.3__0/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.3__0/OMERO5.2__0.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.3__0/delete-ns-orphans.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4DEV__1/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4DEV__2/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4DEV__3/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql creating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4__0/ inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4__0/OMERO5.3__0.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4__0/OMERO5.3__1.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4__0/psql-footer.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4__0/psql-header.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4__0/schema.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/sql/psql/OMERO5.4__0/views.sql inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/test.xml inflating: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/update_dependencies.sh extracting: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/components/antlib/resources/gitversion.xml extracting: openmicroscopy-5.6.3-576-49aa459db9-ice36-b589/components/tools/OmeroCpp/cmake/GitVersion.cmake + rm -f openmicroscopy-5.6.3-576-49aa459db9-ice36-b589.zip + mv /home/omero/workspace/OMERO-test-integration/openmicroscopy-5.6.3-576-49aa459db9-ice36-b589 /home/omero/workspace/OMERO-test-integration/src + source /home/omero/workspace/OMERO-test-integration/.venv3/bin/activate ++ deactivate nondestructive ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ '[' -n '' ']' ++ unset VIRTUAL_ENV ++ unset VIRTUAL_ENV_PROMPT ++ '[' '!' nondestructive = nondestructive ']' ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-test-integration/.venv3 ++ export VIRTUAL_ENV ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ PATH=/home/omero/workspace/OMERO-test-integration/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ export PATH ++ '[' -n '' ']' ++ '[' -z '' ']' ++ _OLD_VIRTUAL_PS1= ++ PS1='(.venv3) ' ++ export PS1 ++ VIRTUAL_ENV_PROMPT='(.venv3) ' ++ export VIRTUAL_ENV_PROMPT ++ hash -r + for x in *.tar.gz + pip install -U omero_dropbox-5.7.1.dev0.tar.gz Processing ./omero_dropbox-5.7.1.dev0.tar.gz Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.3) Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4) Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0) Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.3.5) Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (12.0.0) Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3) Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.6.5) Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.5) Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0) Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.4) Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.11) Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2.6.1) Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2025.11.12) Building wheels for collected packages: omero-dropbox Building wheel for omero-dropbox (pyproject.toml): started Building wheel for omero-dropbox (pyproject.toml): finished with status 'done' Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=392829255b6fe0b1ddc7e04d0fa8b13f0a9d7fca4abf9f594754f79e28e4be64 Stored in directory: /home/omero/.cache/pip/wheels/fc/7e/62/5e5d34b5de7cc5d8ff95a6620b111f491c603301cfe622e998 Successfully built omero-dropbox Installing collected packages: omero-dropbox Successfully installed omero-dropbox-5.7.1.dev0 + for x in *.tar.gz + pip install -U omero_marshal-0.9.2.dev0.tar.gz Processing ./omero_marshal-0.9.2.dev0.tar.gz Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Building wheels for collected packages: omero_marshal Building wheel for omero_marshal (pyproject.toml): started Building wheel for omero_marshal (pyproject.toml): finished with status 'done' Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88122 sha256=3cc1505c8027f301dfb4acc268f00bd09c8548b6abefdca0444f08735f3226d3 Stored in directory: /home/omero/.cache/pip/wheels/19/bc/99/c23dd653c71b3f05e4c008a12495c8f3b095cce849431c54e1 Successfully built omero_marshal Installing collected packages: omero_marshal Attempting uninstall: omero_marshal Found existing installation: omero_marshal 0.9.1 Uninstalling omero_marshal-0.9.1: Successfully uninstalled omero_marshal-0.9.1 Successfully installed omero_marshal-0.9.2.dev0 + for x in *.tar.gz + pip install -U omero_py-5.22.0.dev0.tar.gz Processing ./omero_py-5.22.0.dev0.tar.gz Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (1.4.4) Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (1.0.0) Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (2.3.5) Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (12.0.0) Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (6.0.3) Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (3.6.5) Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (2.32.5) Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (3.2.0) Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.0.dev0) (3.4.4) Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.0.dev0) (3.11) Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.0.dev0) (2.6.1) Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.0.dev0) (2025.11.12) Building wheels for collected packages: omero-py Building wheel for omero-py (pyproject.toml): started Building wheel for omero-py (pyproject.toml): finished with status 'done' Created wheel for omero-py: filename=omero_py-5.22.0.dev0-py3-none-any.whl size=2786250 sha256=bc6ae51f8ecfc5854002c6452d29bc042e853f3575fa6a88c2725c61277187f5 Stored in directory: /home/omero/.cache/pip/wheels/9e/05/9b/8e8bd103e965dc55f7156458690d079677bf95848965ee2e52 Successfully built omero-py Installing collected packages: omero-py Attempting uninstall: omero-py Found existing installation: omero-py 5.21.3 Uninstalling omero-py-5.21.3: Successfully uninstalled omero-py-5.21.3 Successfully installed omero-py-5.22.0.dev0 + for x in *.tar.gz + pip install -U omero_scripts-5.9.2.dev0.tar.gz Processing ./omero_scripts-5.9.2.dev0.tar.gz Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Building wheels for collected packages: omero-scripts Building wheel for omero-scripts (pyproject.toml): started Building wheel for omero-scripts (pyproject.toml): finished with status 'done' Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136991 sha256=627c858f1f59edbccea9acf05de4629868f687dadb2943dc33a5ece0e6944aa0 Stored in directory: /home/omero/.cache/pip/wheels/4c/39/ec/1d35a9b903bbfa62e645ce3b85c00080824fa78bacce0f38d4 Successfully built omero-scripts Installing collected packages: omero-scripts Successfully installed omero-scripts-5.9.2.dev0 + for x in *.tar.gz + pip install -U omero_web-5.30.1.dev0.tar.gz Processing ./omero_web-5.30.1.dev0.tar.gz Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (5.22.0.dev0) Requirement already satisfied: concurrent-log-handler>=0.9.20 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (0.9.28) Requirement already satisfied: Django<5.3,>=5.2.9 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (5.2.9) Requirement already satisfied: django-pipeline in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (4.1.0) Requirement already satisfied: django-cors-headers==3.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (3.7.0) Requirement already satisfied: whitenoise>=5.3.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (6.11.0) Requirement already satisfied: gunicorn>=19.3 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (23.0.0) Requirement already satisfied: omero-marshal>=0.9.1 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (0.9.2.dev0) Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (12.0.0) Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (2025.2) Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (3.2.0) Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (25.0) Requirement already satisfied: importlib-resources in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.1.dev0) (6.5.2) Requirement already satisfied: asgiref>=3.8.1 in ./.venv3/lib64/python3.11/site-packages (from Django<5.3,>=5.2.9->omero-web==5.30.1.dev0) (3.11.0) Requirement already satisfied: sqlparse>=0.3.1 in ./.venv3/lib64/python3.11/site-packages (from Django<5.3,>=5.2.9->omero-web==5.30.1.dev0) (0.5.4) Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.30.1.dev0) (1.4.4) Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.30.1.dev0) (1.0.0) Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.30.1.dev0) (2.3.5) Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.30.1.dev0) (6.0.3) Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.30.1.dev0) (3.6.5) Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.30.1.dev0) (2.32.5) Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.30.1.dev0) (80.9.0) Requirement already satisfied: wheel in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.30.1.dev0) (0.45.1) Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.30.1.dev0) (3.4.4) Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.30.1.dev0) (3.11) Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.30.1.dev0) (2.6.1) Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.30.1.dev0) (2025.11.12) Building wheels for collected packages: omero-web Building wheel for omero-web (pyproject.toml): started Building wheel for omero-web (pyproject.toml): finished with status 'done' Created wheel for omero-web: filename=omero_web-5.30.1.dev0-py3-none-any.whl size=2819088 sha256=a6597dc86108e274cfb242e113b057a6f5aeb96d5b5c6081c1b79c5f6c810e60 Stored in directory: /home/omero/.cache/pip/wheels/72/f1/c1/a13c97397c97ab7b3bf3b05dda300f672650afd6720ede88ba Successfully built omero-web Installing collected packages: omero-web Attempting uninstall: omero-web Found existing installation: omero-web 5.30.0 Uninstalling omero-web-5.30.0: Successfully uninstalled omero-web-5.30.0 Successfully installed omero-web-5.30.1.dev0 + pip install omero-certificates Collecting omero-certificates Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB) Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.22.0.dev0) Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4) Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0) Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.3.5) Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (12.0.0) Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3) Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.6.5) Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.5) Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0) Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.4) Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.11) Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2.6.1) Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2025.11.12) Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB) Installing collected packages: omero-certificates Successfully installed omero-certificates-0.4.0 + for x in omero-cli-duplicate + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate Collecting omero-cli-duplicate Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-p4jlm04i/omero-cli-duplicate_18fe8672422c42e6bd34232433cf8ba0 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-p4jlm04i/omero-cli-duplicate_18fe8672422c42e6bd34232433cf8ba0 Running command git checkout -b merge_ci --track origin/merge_ci Switched to a new branch 'merge_ci' branch 'merge_ci' set up to track 'origin/merge_ci'. Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 551d722288b7c6223e42956274cd87a7a9bd747a Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.22.0.dev0) Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4) Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0) Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.3.5) Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (12.0.0) Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3) Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.6.5) Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.5) Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0) Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.4) Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.11) Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2.6.1) Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2025.11.12) Building wheels for collected packages: omero-cli-duplicate Building wheel for omero-cli-duplicate (pyproject.toml): started Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done' Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=dd3216499a28f1fe52a98955577c238a9969a6523b15c1872b4ddad3ecc304d4 Stored in directory: /tmp/pip-ephem-wheel-cache-kk34xyzu/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46 Successfully built omero-cli-duplicate Installing collected packages: omero-cli-duplicate Successfully installed omero-cli-duplicate-0.4.1.dev0 + pip install -U numpy Requirement already satisfied: numpy in ./.venv3/lib64/python3.11/site-packages (2.3.5) + source /home/omero/workspace/OMERO-test-integration/src/docs/hudson/functions.sh + /home/omero/workspace/OMERO-test-integration/src/build.py build-default test-compile Buildfile: /home/omero/workspace/OMERO-test-integration/src/build.xml check-ivy: Creating /home/omero/workspace/OMERO-test-integration/src/etc/local.properties Created dir: /home/omero/workspace/OMERO-test-integration/src/target :: Apache Ivy 2.4.0 - 20141213170938 :: http://ant.apache.org/ivy/ :: :: loading settings :: file = /home/omero/workspace/OMERO-test-integration/src/etc/ivysettings.xml build-scons: Expanding: /home/omero/workspace/OMERO-test-integration/src/lib/repository/scons-local-2.1.0.zip into /home/omero/workspace/OMERO-test-integration/src/target/scons build: No sub-builds to iterate on Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroWeb... Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroWeb... Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroFS... Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava... tools-init: no-op retrieve: :: Apache Ivy 2.4.0 - 20141213170938 :: http://ant.apache.org/ivy/ :: :: loading settings :: file = /home/omero/workspace/OMERO-test-integration/src/etc/ivysettings.xml WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.apache.ivy.util.url.IvyAuthenticator (file:/home/omero/workspace/OMERO-test-integration/src/lib/repository/ivy-2.4.0.jar) to field java.net.Authenticator.theAuthenticator WARNING: Please consider reporting this to the maintainers of org.apache.ivy.util.url.IvyAuthenticator WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release prepare: Preparing: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/libs Created dir: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated/.done Created dir: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated/src Created dir: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated/resources Created dir: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes Created dir: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/test-classes Created dir: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/reports Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated/resources Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated/resources Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated/resources Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated/resources Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes pre-compile: Expanding: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/libs/glacier2.jar into /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated-classes Expanding: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/libs/ice.jar into /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated-classes Expanding: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/libs/icegrid.jar into /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated-classes Expanding: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/libs/icestorm.jar into /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated-classes Expanding: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/libs/ome-xml.jar into /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated-classes compile: no-op package: Building jar: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/omero_client.jar install: :: delivering :: omero#omero_client;working@31657b3efbee :: 5.6.3-576-49aa459db9-ice36-b589-ice36 :: integration :: Tue Dec 09 00:53:00 UTC 2025 delivering ivy file to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/ivy.xml :: publishing :: omero#omero_client published omero_client to /home/omero/workspace/OMERO-test-integration/src/target/repository/omero/omero_client/5.6.3-576-49aa459db9-ice36-b589-ice36/omero_client-5.6.3-576-49aa459db9-ice36-b589-ice36.jar published ivy to /home/omero/workspace/OMERO-test-integration/src/target/repository/omero/omero_client/5.6.3-576-49aa459db9-ice36-b589-ice36/omero_client-5.6.3-576-49aa459db9-ice36-b589-ice36.xml Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy... Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy... retrieve: :: Apache Ivy 2.4.0 - 20141213170938 :: http://ant.apache.org/ivy/ :: :: loading settings :: file = /home/omero/workspace/OMERO-test-integration/src/etc/ivysettings.xml Entering /home/omero/workspace/OMERO-test-integration/src/components/tools... dist: Created dir: /home/omero/workspace/OMERO-test-integration/src/components/tools/target/service-classes/META-INF Created dir: /home/omero/workspace/OMERO-test-integration/src/components/tools/target/lib/server Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/components/tools/target/downloads/scripts Expanding: /home/omero/workspace/OMERO-test-integration/src/components/tools/target/downloads/scripts/omero_scripts-5.9.2.dev0.tar.gz into /home/omero/workspace/OMERO-test-integration/src/components/tools/target/downloads/scripts Copying 29 files to /home/omero/workspace/OMERO-test-integration/src/components/tools/target/lib/scripts Copying 29 files to /home/omero/workspace/OMERO-test-integration/src/dist Copied 9 empty directories to 1 empty directory under /home/omero/workspace/OMERO-test-integration/src/dist Entering /home/omero/workspace/OMERO-test-integration/src/components/tests... Entering /home/omero/workspace/OMERO-test-integration/src/components/tests/ui... copy-licenses: Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/dist Created dir: /home/omero/workspace/OMERO-test-integration/src/dist/share Copying 44 files to /home/omero/workspace/OMERO-test-integration/src/dist/share copy-history: Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/dist copy-etc: Copying 28 files to /home/omero/workspace/OMERO-test-integration/src/dist/etc Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/dist/etc/templates copy-sql: Copying 60 files to /home/omero/workspace/OMERO-test-integration/src/dist copy-server: conflict on /home/omero/workspace/OMERO-test-integration/src/dist/lib/server/janino.jar in [server]: 3.1.9 won copy-client: Created dir: /home/omero/workspace/OMERO-test-integration/src/dist/lib/client conflict on /home/omero/workspace/OMERO-test-integration/src/dist/lib/client/janino.jar in [client]: 3.1.9 won update-version: Copying 1 file to /home/omero/workspace/OMERO-test-integration/src/dist/etc create-workdirs: Created dir: /home/omero/workspace/OMERO-test-integration/src/dist/etc/grid Created dir: /home/omero/workspace/OMERO-test-integration/src/dist/var Created dir: /home/omero/workspace/OMERO-test-integration/src/dist/var/tmp copy-luts: Created dir: /home/omero/workspace/OMERO-test-integration/src/dist/lib/scripts/luts Copying 47 files to /home/omero/workspace/OMERO-test-integration/src/dist/lib/scripts/luts test-compile: :: loading settings :: file = /home/omero/workspace/OMERO-test-integration/src/etc/ivysettings.xml Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroFS... Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy... Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy... Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroWeb... Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroWeb... Entering /home/omero/workspace/OMERO-test-integration/src/components/tests/ui... Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava... testng-init: :: Apache Ivy 2.4.0 - 20141213170938 :: http://ant.apache.org/ivy/ :: :: loading settings :: file = /home/omero/workspace/OMERO-test-integration/src/etc/ivysettings.xml 00:53:21,799 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.16 00:53:21,801 |-INFO in ch.qos.logback.classic.util.ContextInitializer@137fb1a1 - No custom configurators were discovered as a service. 00:53:21,801 |-INFO in ch.qos.logback.classic.util.ContextInitializer@137fb1a1 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator 00:53:21,805 |-INFO in ch.qos.logback.classic.util.ContextInitializer@137fb1a1 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator 00:53:21,805 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] 00:53:21,805 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] 00:53:21,806 |-INFO in ch.qos.logback.classic.util.ContextInitializer@137fb1a1 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY 00:53:21,806 |-INFO in ch.qos.logback.classic.util.ContextInitializer@137fb1a1 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator 00:53:21,808 |-INFO in ch.qos.logback.classic.util.ContextInitializer@137fb1a1 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator 00:53:21,808 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] 00:53:21,808 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes/logback.xml] 00:53:21,809 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@6cbd57fa - Resource [logback.xml] occurs multiple times on the classpath. 00:53:21,809 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@6cbd57fa - Resource [logback.xml] occurs at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes/logback.xml] 00:53:21,809 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@6cbd57fa - Resource [logback.xml] occurs at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated/resources/logback.xml] 00:53:22,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stderr] 00:53:22,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] 00:53:22,060 |-INFO in ch.qos.logback.core.model.processor.ImplicitModelHandler - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property 00:53:22,062 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@64513b46 - As of version 1.2.0 "immediateFlush" property should be set within the enclosing Appender. 00:53:22,062 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@64513b46 - Please move "immediateFlush" property into the enclosing appender. 00:53:22,121 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@64513b46 - Setting the "immediateFlush" property of the enclosing appender to true 00:53:22,122 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [velocity] to ERROR 00:53:22,122 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org] to ERROR 00:53:22,122 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [ome] to ERROR 00:53:22,122 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci] to ERROR 00:53:22,122 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to WARN 00:53:22,122 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stderr] to Logger[ROOT] 00:53:22,123 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@66b1f207 - End of configuration. 00:53:22,125 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@82da5c9 - Registering current configuration as safe fallback point 00:53:22,125 |-INFO in ch.qos.logback.classic.util.ContextInitializer@137fb1a1 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 317 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY lifecycle.test-compile: Copying 3 files to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/test-classes Compiling 85 source files to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/test-classes warning: [options] bootstrap class path not set in conjunction with -source 8 /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/AbstractServerTest.java:61: warning: [deprecation] RawAccessRequest in omero.grid has been deprecated import omero.grid.RawAccessRequest; ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/DeleteServiceFilesTest.java:32: warning: [deprecation] RawAccessRequest in omero.grid has been deprecated import omero.grid.RawAccessRequest; ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ManagedRepositoryTest.java:53: warning: [deprecation] RawAccessRequest in omero.grid has been deprecated import omero.grid.RawAccessRequest; ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:31: warning: [deprecation] ImportJob in omero.model has been deprecated import omero.model.ImportJob; ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:32: warning: [deprecation] ImportJobI in omero.model has been deprecated import omero.model.ImportJobI; ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ModelMockFactory.java:1206: warning: [deprecation] newInstance() in Class has been deprecated IObject link = (IObject) linkClass.newInstance(); ^ where T is a type-variable: T extends Object declared in class Class /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/CreatePojosFixture2.java:269: warning: [deprecation] newInstance() in Class has been deprecated T copy = (T) obj.getClass().newInstance(); ^ where T is a type-variable: T extends Object declared in class Class /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/DeleteServiceFilesTest.java:418: warning: [deprecation] RawAccessRequest in omero.grid has been deprecated RawAccessRequest raw = new RawAccessRequest(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/DeleteServiceFilesTest.java:418: warning: [deprecation] RawAccessRequest in omero.grid has been deprecated RawAccessRequest raw = new RawAccessRequest(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/DeleteServiceFilesTest.java:419: warning: [deprecation] repoUuid in RawAccessRequest has been deprecated raw.repoUuid = legacy.root().getHash().getValue(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/DeleteServiceFilesTest.java:420: warning: [deprecation] command in RawAccessRequest has been deprecated raw.command = "rm"; ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/DeleteServiceFilesTest.java:421: warning: [deprecation] args in RawAccessRequest has been deprecated raw.args = Arrays.asList(path); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/DiskUsageTest.java:156: warning: [deprecation] newInstance() in Class has been deprecated final IObject link = linkClass.newInstance(); ^ where T is a type-variable: T extends Object declared in class Class /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/DuplicationTest.java:1332: warning: [deprecation] newInstance() in Class has been deprecated originalLink.setChild(annotationClass.newInstance()); ^ where T is a type-variable: T extends Object declared in class Class /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ImporterTest.java:1088: warning: [deprecation] findByImage(long,RoiOptions) in IRoiPrx has been deprecated RoiResult r = svc.findByImage(id, new RoiOptions()); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ManagedRepositoryTest.java:900: warning: [deprecation] RawAccessRequest in omero.grid has been deprecated final RawAccessRequest request = new RawAccessRequest(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ManagedRepositoryTest.java:900: warning: [deprecation] RawAccessRequest in omero.grid has been deprecated final RawAccessRequest request = new RawAccessRequest(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ManagedRepositoryTest.java:901: warning: [deprecation] repoUuid in RawAccessRequest has been deprecated request.repoUuid = repo.root().getHash().getValue(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ManagedRepositoryTest.java:902: warning: [deprecation] command in RawAccessRequest has been deprecated request.command = "exists"; ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ManagedRepositoryTest.java:903: warning: [deprecation] args in RawAccessRequest has been deprecated request.args = Collections.singletonList(dirPath); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ManagedRepositoryTest.java:939: warning: [deprecation] RawAccessRequest in omero.grid has been deprecated final RawAccessRequest request = new RawAccessRequest(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ManagedRepositoryTest.java:939: warning: [deprecation] RawAccessRequest in omero.grid has been deprecated final RawAccessRequest request = new RawAccessRequest(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ManagedRepositoryTest.java:940: warning: [deprecation] repoUuid in RawAccessRequest has been deprecated request.repoUuid = repo.root().getHash().getValue(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ManagedRepositoryTest.java:941: warning: [deprecation] command in RawAccessRequest has been deprecated request.command = "exists"; ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ManagedRepositoryTest.java:942: warning: [deprecation] args in RawAccessRequest has been deprecated request.args = Collections.singletonList(dirName); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:255: warning: [deprecation] ImportJob in omero.model has been deprecated final ImportJob importJob = new ImportJobI(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:255: warning: [deprecation] ImportJobI in omero.model has been deprecated final ImportJob importJob = new ImportJobI(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:266: warning: [deprecation] setImageName(RString) in ImportJob has been deprecated importJob.setImageName(omero.rtypes.rstring(name)); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:268: warning: [deprecation] setImageDescription(RString) in ImportJob has been deprecated importJob.setImageDescription(omero.rtypes.rstring(desc)); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:273: warning: [deprecation] ImportJob in omero.model has been deprecated ImportJob sent = (ImportJob) iUpdate.saveAndReturnObject(importJob); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:273: warning: [deprecation] ImportJob in omero.model has been deprecated ImportJob sent = (ImportJob) iUpdate.saveAndReturnObject(importJob); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:274: warning: [deprecation] getImageName() in ImportJob has been deprecated final String savedName = sent.getImageName().getValue().toString(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:275: warning: [deprecation] getImageDescription() in ImportJob has been deprecated final String savedDesc = sent.getImageDescription().getValue().toString(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:277: warning: [deprecation] ImportJob in omero.model has been deprecated final ImportJob retrievedImportJob = (ImportJob) iQuery.get("ImportJob", id); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:277: warning: [deprecation] ImportJob in omero.model has been deprecated final ImportJob retrievedImportJob = (ImportJob) iQuery.get("ImportJob", id); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:278: warning: [deprecation] getImageName() in ImportJob has been deprecated final String retrievedName = retrievedImportJob.getImageName().getValue().toString(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/ObjectPropertiesTest.java:279: warning: [deprecation] getImageDescription() in ImportJob has been deprecated final String retrievedDesc = retrievedImportJob.getImageDescription().getValue().toString(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:141: warning: [deprecation] findByImage(long,RoiOptions) in IRoiPrx has been deprecated RoiResult r = svc.findByImage(image.getId().getValue(), ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:190: warning: [deprecation] getRoiMeasurements(long,RoiOptions) in IRoiPrx has been deprecated List l = svc.getRoiMeasurements(image.getId().getValue(), ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:220: warning: [deprecation] getRoiMeasurements(long,RoiOptions) in IRoiPrx has been deprecated l = svc.getRoiMeasurements(image.getId().getValue(), options); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:241: warning: [deprecation] getRoiMeasurements(long,RoiOptions) in IRoiPrx has been deprecated l = svc.getRoiMeasurements(image.getId().getValue(), options); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:313: warning: [deprecation] getRoiMeasurements(long,RoiOptions) in IRoiPrx has been deprecated List l = svc.getRoiMeasurements(image.getId().getValue(), ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:320: warning: [deprecation] getMeasuredRoisMap(long,List,RoiOptions) in IRoiPrx has been deprecated Map values = svc.getMeasuredRoisMap(image.getId() ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:386: warning: [deprecation] getRoiMeasurements(long,RoiOptions) in IRoiPrx has been deprecated List l = svc.getRoiMeasurements(image.getId().getValue(), ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:390: warning: [deprecation] getTable(long) in IRoiPrx has been deprecated table = svc.getTable(f.getId().getValue()); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:412: warning: [deprecation] findByImage(long,RoiOptions) in IRoiPrx has been deprecated RoiResult r = svc.findByImage(image.getId().getValue(), ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:426: warning: [deprecation] findByRoi(long,RoiOptions) in IRoiPrx has been deprecated r = svc.findByRoi(r1.getId().getValue(), new RoiOptions()); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:437: warning: [deprecation] findByRoi(long,RoiOptions) in IRoiPrx has been deprecated r = svc.findByRoi(r2.getId().getValue(), new RoiOptions()); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:448: warning: [deprecation] findByPlane(long,int,int,RoiOptions) in IRoiPrx has been deprecated r = svc.findByPlane(image.getId().getValue(), 1, 0, new RoiOptions()); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:459: warning: [deprecation] findByPlane(long,int,int,RoiOptions) in IRoiPrx has been deprecated r = svc.findByPlane(image.getId().getValue(), 1, 1, new RoiOptions()); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:733: warning: [deprecation] Integer(int) in Integer has been deprecated null, new Integer(0), new Integer(0), new int[] {0}, "null ids"}); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:733: warning: [deprecation] Integer(int) in Integer has been deprecated null, new Integer(0), new Integer(0), new int[] {0}, "null ids"}); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:735: warning: [deprecation] Integer(int) in Integer has been deprecated new ArrayList(), new Integer(0), new Integer(0), new int[] {0}, ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:735: warning: [deprecation] Integer(int) in Integer has been deprecated new ArrayList(), new Integer(0), new Integer(0), new int[] {0}, ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:738: warning: [deprecation] Long(long) in Long has been deprecated Arrays.asList(new Long[] {new Long (-1)}), new Integer(0), new Integer(0), ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:738: warning: [deprecation] Integer(int) in Integer has been deprecated Arrays.asList(new Long[] {new Long (-1)}), new Integer(0), new Integer(0), ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:738: warning: [deprecation] Integer(int) in Integer has been deprecated Arrays.asList(new Long[] {new Long (-1)}), new Integer(0), new Integer(0), ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:740: warning: [deprecation] Integer(int) in Integer has been deprecated inputs.add(new Object[] { ids, new Integer(10), new Integer(10), new int[] {0}, ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:740: warning: [deprecation] Integer(int) in Integer has been deprecated inputs.add(new Object[] { ids, new Integer(10), new Integer(10), new int[] {0}, ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:742: warning: [deprecation] Integer(int) in Integer has been deprecated inputs.add(new Object[] { ids, new Integer(0), new Integer(-10), new int[] {0}, ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:742: warning: [deprecation] Integer(int) in Integer has been deprecated inputs.add(new Object[] { ids, new Integer(0), new Integer(-10), new int[] {0}, ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:744: warning: [deprecation] Integer(int) in Integer has been deprecated inputs.add(new Object[] { ids, new Integer(0), new Integer(0), new int[] {200}, ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:744: warning: [deprecation] Integer(int) in Integer has been deprecated inputs.add(new Object[] { ids, new Integer(0), new Integer(0), new int[] {200}, ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:746: warning: [deprecation] Integer(int) in Integer has been deprecated inputs.add(new Object[] { ids, new Integer(0), new Integer(0), null, ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:746: warning: [deprecation] Integer(int) in Integer has been deprecated inputs.add(new Object[] { ids, new Integer(0), new Integer(0), null, ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:748: warning: [deprecation] Integer(int) in Integer has been deprecated inputs.add(new Object[] { ids, new Integer(0), new Integer(0), new int[] {}, ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:748: warning: [deprecation] Integer(int) in Integer has been deprecated inputs.add(new Object[] { ids, new Integer(0), new Integer(0), new int[] {}, ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:755: warning: [deprecation] getShapeStatsRestricted(List,int,int,int[]) in IRoiPrx has been deprecated svc.getShapeStatsRestricted( ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/RoiServiceTest.java:764: warning: [deprecation] getShapeStatsRestricted(List,int,int,int[]) in IRoiPrx has been deprecated final ShapeStats [] stats = svc.getShapeStatsRestricted(ids, 0, 0, new int[] {0}); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/chgrp/HierarchyMoveTest.java:1030: warning: [deprecation] setRelatedTo(Pixels) in Pixels has been deprecated projection.getPrimaryPixels().setRelatedTo((Pixels) original.getPrimaryPixels().proxy()); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/AnnotationDeleteTest.java:478: warning: [deprecation] typesToIgnore in Delete2 has been deprecated request.typesToIgnore = Collections.singletonList("TagAnnotation"); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/AnnotationDeleteTest.java:495: warning: [deprecation] typesToIgnore in Delete2 has been deprecated request.typesToIgnore = Collections.singletonList("IAnnotationLink"); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/AnnotationDeleteTest.java:501: warning: [deprecation] typesToIgnore in Delete2 has been deprecated request.typesToIgnore = Collections.singletonList("Annotation"); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/AnnotationDeleteTest.java:547: warning: [deprecation] typesToIgnore in Delete2 has been deprecated request.typesToIgnore = Collections.singletonList("Annotation"); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/HierarchyDeleteTest.java:537: warning: [deprecation] setRelatedTo(Pixels) in Pixels has been deprecated projection.getPrimaryPixels().setRelatedTo((Pixels) original.getPrimaryPixels().proxy()); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/RelatedToTest.java:37: warning: [deprecation] setRelatedTo(Pixels) in Pixels has been deprecated p2.setRelatedTo(p1); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/RelatedToTest.java:39: warning: [deprecation] getRelatedTo() in Pixels has been deprecated Assert.assertEquals(p1.getId(), p2.getRelatedTo().getId()); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/RelatedToTest.java:66: warning: [deprecation] setRelatedTo(Pixels) in Pixels has been deprecated pixels1.setRelatedTo(pixels2); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/RelatedToTest.java:68: warning: [deprecation] getRelatedTo() in Pixels has been deprecated Pixels pixels = pixels1.getRelatedTo(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/RelatedToTest.java:88: warning: [deprecation] getRelatedTo() in Pixels has been deprecated Assert.assertNull(pixels1.getRelatedTo()); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/RelatedToTest.java:106: warning: [deprecation] setRelatedTo(Pixels) in Pixels has been deprecated pixels1.setRelatedTo(pixels2); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/RelatedToTest.java:108: warning: [deprecation] getRelatedTo() in Pixels has been deprecated Pixels pixels = pixels1.getRelatedTo(); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/RelatedToTest.java:128: warning: [deprecation] getRelatedTo() in Pixels has been deprecated Assert.assertNull(pixels1.getRelatedTo()); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/RoiDeleteTest.java:113: warning: [deprecation] getRoiMeasurements(long,RoiOptions) in IRoiPrx has been deprecated List l = svc.getRoiMeasurements(image.getId().getValue(), ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/RoiDeleteTest.java:147: warning: [deprecation] getRoiMeasurements(long,RoiOptions) in IRoiPrx has been deprecated l = svc.getRoiMeasurements(image.getId().getValue(), options); ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/RoiDeleteTest.java:186: warning: [deprecation] getRoiMeasurements(long,RoiOptions) in IRoiPrx has been deprecated List l = svc.getRoiMeasurements(image.getId().getValue(), ^ /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/test/integration/delete/RoiDeleteTest.java:221: warning: [deprecation] getRoiMeasurements(long,RoiOptions) in IRoiPrx has been deprecated l = svc.getRoiMeasurements(image.getId().getValue(), options); ^ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 88 warnings Deleting: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/_omero_build_1517269322.tmp Building jar: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/OmeroJava-test.jar :: loading settings :: file = /home/omero/workspace/OMERO-test-integration/src/etc/ivysettings.xml :: delivering :: omero#OmeroJava-test;working@31657b3efbee :: 5.6.3-576-49aa459db9-ice36-b589-ice36 :: integration :: Tue Dec 09 00:53:19 UTC 2025 delivering ivy file to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/OmeroJava-test.xml :: publishing :: omero#OmeroJava-test published OmeroJava-test to /home/omero/workspace/OMERO-test-integration/src/target/test-repository/OmeroJava-test-5.6.3-576-49aa459db9-ice36-b589-ice36.jar published ivy to /home/omero/workspace/OMERO-test-integration/src/target/test-repository/OmeroJava-test-5.6.3-576-49aa459db9-ice36-b589-ice36.xml BUILD SUCCESSFUL Total time: 28 seconds + OMERO_DIST=/home/omero/workspace/OMERO-test-integration/src/dist + export OMERODIR=/home/omero/workspace/OMERO-test-integration/src/dist + OMERODIR=/home/omero/workspace/OMERO-test-integration/src/dist + omero config set omero.db.name OMERO-test-integration + omero config set omero.db.host pg + omero config set omero.db.user postgres + omero config set omero.db.poolsize 50 + omero config set omero.jvmcfg.max_system_memory.blitz 64000 + omero config set omero.data.dir /home/omero/workspace/OMERO-test-integration/data + omero config set omero.ports.prefix 1 + omero config set omero.web.server_list '[["testintegration",14064,"testintegration"]]' + omero certificates OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024) certificates created: /home/omero/workspace/OMERO-test-integration/data/certs/server.key /home/omero/workspace/OMERO-test-integration/data/certs/server.pem /home/omero/workspace/OMERO-test-integration/data/certs/server.p12 + createdb -h pg -U postgres OMERO-test-integration + omero db script -f dbsetup.sql '' '' omero WARNING: Positional arguments are deprecated Using OMERO5.4 for version Using 0 for patch Using password from commandline + psql -h pg -U postgres -d OMERO-test-integration -f dbsetup.sql BEGIN CREATE FUNCTION CREATE FUNCTION assert_db_server_prerequisites -------------------------------- (1 row) DROP FUNCTION DROP FUNCTION CREATE DOMAIN CREATE DOMAIN CREATE DOMAIN CREATE DOMAIN CREATE DOMAIN CREATE TYPE CREATE TYPE CREATE TYPE CREATE TYPE CREATE TYPE CREATE TYPE CREATE TYPE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE CREATE TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE psql:dbsetup.sql:2842: NOTICE: identifier "fkcontraststretchingcontext_codomainmapcontext_id_codomainmapcontext" will be truncated to "fkcontraststretchingcontext_codomainmapcontext_id_codomainmapco" ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE psql:dbsetup.sql:4712: NOTICE: identifier "fklogicalchannel_photometricinterpretation_photometricinterpretation" will be truncated to "fklogicalchannel_photometricinterpretation_photometricinterpret" ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE psql:dbsetup.sql:5697: NOTICE: identifier "fkreverseintensitycontext_codomainmapcontext_id_codomainmapcontext" will be truncated to "fkreverseintensitycontext_codomainmapcontext_id_codomainmapcont" ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE CREATE TABLE DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW DROP TABLE CREATE VIEW CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX 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CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX 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CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE FUNCTION SET CONSTRAINTS CREATE FUNCTION CREATE SEQUENCE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE CREATE INDEX CREATE FUNCTION CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE SEQUENCE INSERT 0 1 CREATE FUNCTION CREATE FUNCTION CREATE FUNCTION CREATE TABLE CREATE INDEX CREATE INDEX CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE FUNCTION CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE FUNCTION CREATE FUNCTION CREATE FUNCTION CREATE FUNCTION CREATE FUNCTION CREATE FUNCTION CREATE FUNCTION CREATE FUNCTION CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER ALTER TABLE ALTER TABLE ALTER TABLE INSERT 0 1 ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 UPDATE 1 UPDATE 1 ALTER TABLE ALTER TABLE ALTER TABLE INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 INSERT 0 1 UPDATE 1 UPDATE 1 UPDATE 1 UPDATE 1 UPDATE 1 UPDATE 1 UPDATE 1 UPDATE 1 UPDATE 1 UPDATE 1 UPDATE 1 ALTER TABLE CREATE FUNCTION CREATE TABLE INSERT 0 1 ALTER TABLE ALTER TABLE ALTER TABLE CREATE INDEX ALTER TABLE ALTER TABLE CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX ALTER TABLE CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE TABLE INSERT 0 1 INSERT 0 1 CREATE TABLE INSERT 0 1 CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE TRIGGER CREATE TABLE CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE INDEX CREATE FUNCTION CREATE TRIGGER ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE CREATE FUNCTION CREATE TRIGGER CREATE FUNCTION CREATE FUNCTION CREATE FUNCTION CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER DROP TABLE DROP TABLE DROP TABLE DROP TABLE DROP TABLE CREATE VIEW CREATE VIEW CREATE VIEW CREATE VIEW CREATE VIEW ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE ALTER TABLE CREATE FUNCTION CREATE TRIGGER CREATE TABLE CREATE INDEX CREATE FUNCTION CREATE FUNCTION CREATE FUNCTION CREATE FUNCTION CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE TRIGGER CREATE FUNCTION CREATE FUNCTION CREATE TRIGGER CREATE TRIGGER CREATE INDEX UPDATE 1 COMMIT + rm dbsetup.sql + export OMERO_PROFILE=/home/omero/workspace/OMERO-test-integration/config + OMERO_PROFILE=/home/omero/workspace/OMERO-test-integration/config + mkdir -p /home/omero/workspace/OMERO-test-integration/config/blitz + cp /home/omero/workspace/OMERO-test-integration/src/dist/etc/blitz/mail-senders.example /home/omero/workspace/OMERO-test-integration/src/dist/etc/blitz/mail-server.example /home/omero/workspace/OMERO-test-integration/config/blitz + for f in $OMERO_PROFILE/blitz/* ++ basename /home/omero/workspace/OMERO-test-integration/config/blitz/mail-senders.example .example + mv /home/omero/workspace/OMERO-test-integration/config/blitz/mail-senders.example /home/omero/workspace/OMERO-test-integration/config/blitz/mail-senders.xml + for f in $OMERO_PROFILE/blitz/* ++ basename /home/omero/workspace/OMERO-test-integration/config/blitz/mail-server.example .example + mv /home/omero/workspace/OMERO-test-integration/config/blitz/mail-server.example /home/omero/workspace/OMERO-test-integration/config/blitz/mail-server.xml + omero config set omero.mail.config true + omero config set omero.mail.fake true + omero config set omero.mail.port 2525 + BUILD_ID=DONT_KILL_ME + omero admin start No descriptor given. Using etc/grid/default.xml Creating /home/omero/workspace/OMERO-test-integration/src/dist/var/master Initializing /home/omero/workspace/OMERO-test-integration/src/dist/var/log Creating /home/omero/workspace/OMERO-test-integration/src/dist/var/registry Waiting on startup. Use CTRL-C to exit + omero admin waitup Waiting on startup. Use CTRL-C to exit + omero admin diagnostics ================================================================================ OMERO Diagnostics (admin) ================================================================================ Commands: java -version 11.0.25 (/usr/bin/java) Commands: python -V 3.11.9 (/home/omero/workspace/OMERO-test-integration/.venv3/bin/python) Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode) Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin) Commands: psql --version 16.8 (/usr/bin/psql) Commands: openssl version 3.2.24 (/usr/bin/openssl) Component: OMERO.py 5.22.0.dev0 Component: OMERO.server 5.6.3-576-49aa459db9-ice36-b589-ice36 Server: icegridnode running Server: Blitz-0 active (pid = 2115086, enabled) Server: DropBox activating (enabled) Server: FileServer active (pid = 2115178, enabled) Server: Indexer-0 activating (enabled) Server: MonitorServer active (pid = 2115123, enabled) Server: OMERO.Glacier2 active (pid = 2115180, enabled) Server: OMERO.IceStorm active (pid = 2115130, enabled) Server: PixelData-0 activating (enabled) Server: Processor-0 activating (enabled) Server: Tables-0 activating (enabled) Server: TestDropBox inactive (enabled) Log dir: /home/omero/workspace/OMERO-test-integration/src/dist/var/log exists Log files: Blitz-0.log 135.9 KB errors=0 warnings=3 Log files: DropBox.log 121 B Log files: FileServer.log 114 B Log files: Indexer-0.log 114 B Log files: MonitorServer.log 117 B Log files: PixelData-0.log 114 B Log files: Processor-0.log 281 B Log files: Tables-0.log 281 B Log files: TestDropBox.log n/a Log files: master.err 605 B Log files: master.out 42.0 KB Log files: Total size 0.18 MB Environment:OMERO_HOME=(unset) Environment:OMERODIR=/home/omero/workspace/OMERO-test-integration/src/dist Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:OMERO_USERDIR=(unset) Environment:OMERO_TMPDIR=(unset) Environment:PATH=/home/omero/workspace/OMERO-test-integration/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin Environment:PYTHONPATH=(unset) Environment:ICE_HOME=/opt/ice-3.6.5 Environment:LD_LIBRARY_PATH=(unset) Environment:DYLD_LIBRARY_PATH=(unset) OMERO SSL port:14064 OMERO TCP port:14063 OMERO data dir:'/home/omero/workspace/OMERO-test-integration/data' Exists? True Is writable? True OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 693927) JVM settings: Blitz-${index} -Xmx9600m JVM settings: Indexer-${index} -Xmx4800m JVM settings: PixelData-${index} -Xmx7200m JVM settings: Repository-${index} -Xmx4800m Jar: lib/server/formats-api.jar Bio-Formats API 8.4.0-SNAPSHOT 9 December 2025 26fd5a143365bab40e31a18ef4b27e020715f445 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.4.0-SNAPSHOT 9 December 2025 26fd5a143365bab40e31a18ef4b27e020715f445 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.4.0-SNAPSHOT 9 December 2025 26fd5a143365bab40e31a18ef4b27e020715f445 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.3-SNAPSHOT 9 December 2025 3b4abf52657011bfbbe1f707ccb3135a045299cc Jar: lib/server/ome-common.jar OME Common Java 6.1.2-SNAPSHOT 9 December 2025 3b4abf52657011bfbbe1f707ccb3135a045299cc Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 9 December 2025 3b4abf52657011bfbbe1f707ccb3135a045299cc Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 9 December 2025 3b4abf52657011bfbbe1f707ccb3135a045299cc Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 9 December 2025 3b4abf52657011bfbbe1f707ccb3135a045299cc Jar: lib/server/ome-xml.jar OME XML library 6.5.2-SNAPSHOT 9 December 2025 3b4abf52657011bfbbe1f707ccb3135a045299cc Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT Jar: lib/server/omero-gateway.jar jar 5.10.5-SNAPSHOT Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT + export OMERO_SESSION_DIR=/tmp/OMERO-test-integration/554 + OMERO_SESSION_DIR=/tmp/OMERO-test-integration/554 + export ICE_CONFIG=/home/omero/workspace/OMERO-test-integration/src/dist/etc/ice.config + ICE_CONFIG=/home/omero/workspace/OMERO-test-integration/src/dist/etc/ice.config + echo Running the integration tests with -Dtestng.useDefaultListeners=true Running the integration tests with -Dtestng.useDefaultListeners=true + /home/omero/workspace/OMERO-test-integration/src/build.py -f components/tools/OmeroJava/build.xml -Dtestng.useDefaultListeners=true -Dtestreports.dir=target/reports/integration integration Buildfile: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/build.xml Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava... testng-init: :: Apache Ivy 2.4.0 - 20141213170938 :: http://ant.apache.org/ivy/ :: :: loading settings :: file = /home/omero/workspace/OMERO-test-integration/src/etc/ivysettings.xml 00:54:01,988 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.16 00:54:01,991 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - No custom configurators were discovered as a service. 00:54:01,991 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator 00:54:01,995 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator 00:54:01,995 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] 00:54:01,996 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] 00:54:01,997 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY 00:54:01,997 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator 00:54:01,998 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator 00:54:01,999 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] 00:54:01,999 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes/logback.xml] 00:54:02,001 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@5fffb692 - Resource [logback.xml] occurs multiple times on the classpath. 00:54:02,001 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@5fffb692 - Resource [logback.xml] occurs at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes/logback.xml] 00:54:02,001 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@5fffb692 - Resource [logback.xml] occurs at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated/resources/logback.xml] 00:54:02,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stderr] 00:54:02,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] 00:54:02,239 |-INFO in ch.qos.logback.core.model.processor.ImplicitModelHandler - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property 00:54:02,241 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@48cb2d73 - As of version 1.2.0 "immediateFlush" property should be set within the enclosing Appender. 00:54:02,241 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@48cb2d73 - Please move "immediateFlush" property into the enclosing appender. 00:54:02,301 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@48cb2d73 - Setting the "immediateFlush" property of the enclosing appender to true 00:54:02,302 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [velocity] to ERROR 00:54:02,302 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org] to ERROR 00:54:02,302 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [ome] to ERROR 00:54:02,302 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci] to ERROR 00:54:02,302 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to WARN 00:54:02,302 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stderr] to Logger[ROOT] 00:54:02,303 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@243bf087 - End of configuration. 00:54:02,306 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@3086f480 - Registering current configuration as safe fallback point 00:54:02,306 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 308 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY lifecycle.test-compile: Deleting: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/_omero_build_905657311.tmp Deleting: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/OmeroJava-test.xml :: loading settings :: file = /home/omero/workspace/OMERO-test-integration/src/etc/ivysettings.xml :: delivering :: omero#OmeroJava-test;working@31657b3efbee :: 5.6.3-576-49aa459db9-ice36-b589-ice36 :: integration :: Tue Dec 09 00:53:58 UTC 2025 delivering ivy file to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/OmeroJava-test.xml :: publishing :: omero#OmeroJava-test published OmeroJava-test to /home/omero/workspace/OMERO-test-integration/src/target/test-repository/OmeroJava-test-5.6.3-576-49aa459db9-ice36-b589-ice36.jar published ivy to /home/omero/workspace/OMERO-test-integration/src/target/test-repository/OmeroJava-test-5.6.3-576-49aa459db9-ice36-b589-ice36.xml integration: 00:54:02,844 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.16 00:54:02,847 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - No custom configurators were discovered as a service. 00:54:02,847 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator 00:54:02,848 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator 00:54:02,849 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] 00:54:02,850 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] 00:54:02,850 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY 00:54:02,850 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator 00:54:02,851 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator 00:54:02,852 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] 00:54:02,852 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes/logback.xml] 00:54:02,853 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@9f116cc - Resource [logback.xml] occurs multiple times on the classpath. 00:54:02,853 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@9f116cc - Resource [logback.xml] occurs at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes/logback.xml] 00:54:02,853 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@9f116cc - Resource [logback.xml] occurs at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated/resources/logback.xml] 00:54:03,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stderr] 00:54:03,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] 00:54:03,065 |-INFO in ch.qos.logback.core.model.processor.ImplicitModelHandler - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property 00:54:03,066 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@12468a38 - As of version 1.2.0 "immediateFlush" property should be set within the enclosing Appender. 00:54:03,066 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@12468a38 - Please move "immediateFlush" property into the enclosing appender. 00:54:03,093 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@12468a38 - Setting the "immediateFlush" property of the enclosing appender to true 00:54:03,093 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [velocity] to ERROR 00:54:03,093 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org] to ERROR 00:54:03,093 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [ome] to ERROR 00:54:03,093 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci] to ERROR 00:54:03,094 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to WARN 00:54:03,094 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stderr] to Logger[ROOT] 00:54:03,094 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1aa7ecca - End of configuration. 00:54:03,095 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@59309333 - Registering current configuration as safe fallback point 00:54:03,095 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 244 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY 05fa6f40-a409-4bea-8ad6-7695bb716585 -! 12/9/25 00:58:25:777 warning: Ice.ThreadPool.Client-0: dispatch exception: identity: M,7%MAGFP:^22^7Twb}a/4fd0b4a5-b5c8-4e9e-a8a8-fb2631a3309b facet: operation: finished remote host: 127.0.0.1 remote port: 14064 java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0 at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64) at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70) at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248) at java.base/java.util.Objects.checkIndex(Objects.java:374) at java.base/java.util.ArrayList.remove(ArrayList.java:536) at ome.xml.model.ReferenceList.remove(ReferenceList.java:102) at ome.xml.model.ReferenceList.set(ReferenceList.java:129) at ome.xml.model.Image.setLinkedAnnotation(Image.java:687) at ome.xml.meta.OMEXMLMetadataImpl.setImageAnnotationRef(OMEXMLMetadataImpl.java:8046) at ome.xml.meta.MetadataConverter.convertImages(MetadataConverter.java:1340) at ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:99) at loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924) at loci.formats.in.OMEXMLReader.initFile(OMEXMLReader.java:331) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=Index 1 out of bounds for length 0} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 00:59:19,701 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 00:59:36,258 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 00:59:39,247 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:00:13,977 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:00:30,424 ERROR [ ome.formats.importer.ImportLibrary] (sDataset-1) Cannot link to target 2025-12-09 01:00:32,244 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted -! 12/9/25 01:00:33:520 warning: Ice.ThreadPool.Client-0: dispatch exception: identity: Otn^6O7%\'Q.:ZOV[\'-^H/d26f931b-1b0a-4f72-b4b7-fbb79f4885bc facet: operation: finished remote host: 127.0.0.1 remote port: 14064 java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0 at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64) at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70) at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248) at java.base/java.util.Objects.checkIndex(Objects.java:374) at java.base/java.util.ArrayList.remove(ArrayList.java:536) at ome.xml.model.ReferenceList.remove(ReferenceList.java:102) at ome.xml.model.ReferenceList.set(ReferenceList.java:129) at ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341) at ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003) at ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426) at ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100) at loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924) at loci.formats.in.OMEXMLReader.initFile(OMEXMLReader.java:331) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=Index 1 out of bounds for length 0} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) -! 12/9/25 01:02:36:294 warning: Ice.ThreadPool.Client-0: dispatch exception: identity: VT_k$k$]Z[\'~{K5l|I)0/a94ab6e3-4a4e-4f32-a6b0-2e19cf93954c facet: operation: finished remote host: 127.0.0.1 remote port: 14064 java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0 at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64) at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70) at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248) at java.base/java.util.Objects.checkIndex(Objects.java:374) at java.base/java.util.ArrayList.remove(ArrayList.java:536) at ome.xml.model.ReferenceList.remove(ReferenceList.java:102) at ome.xml.model.ReferenceList.set(ReferenceList.java:129) at ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341) at ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003) at ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426) at ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100) at loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924) at loci.formats.in.OMEXMLReader.initFile(OMEXMLReader.java:331) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=Index 1 out of bounds for length 0} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 01:02:55,318 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:02:56,250 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:02:57,104 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:00,885 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:01,769 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:02,298 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:02,874 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:03,470 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:04,011 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:04,612 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:05,326 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:05,884 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:06,453 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:07,037 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:07,575 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:08,142 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:08,716 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:09,226 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:09,782 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:10,351 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:10,878 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:11,443 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:12,165 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:12,687 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:13,394 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:13,965 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:14,472 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:15,042 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:15,726 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:16,349 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:17,009 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:17,690 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:18,326 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:18,988 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:19,801 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:20,421 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:21,087 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:21,762 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:22,397 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:03:25,589 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted -! 12/9/25 01:04:36:479 warning: Ice.ThreadPool.Client-0: dispatch exception: identity: \",xX>PX+k>QR7_xR<[#A/d674548d-fac6-4f0f-a11e-04c4dd464fe4 facet: operation: finished remote host: 127.0.0.1 remote port: 14064 java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0 at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64) at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70) at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248) at java.base/java.util.Objects.checkIndex(Objects.java:374) at java.base/java.util.ArrayList.remove(ArrayList.java:536) at ome.xml.model.ReferenceList.remove(ReferenceList.java:102) at ome.xml.model.ReferenceList.set(ReferenceList.java:129) at ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341) at ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003) at ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426) at ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100) at loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924) at loci.formats.in.OMEXMLReader.initFile(OMEXMLReader.java:331) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=Index 1 out of bounds for length 0} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 01:05:25,800 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:05:27,191 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:05:28,366 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:05:29,313 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:05:30,412 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:05:30,823 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:05:32,147 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:05:33,320 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:07:33,527 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:07:34,832 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:07:36,023 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:09:36,237 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:11:36,440 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:11:37,290 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:11:38,072 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:11:39,006 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:13:01,103 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:13:02,634 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:13:04,050 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:13:05,474 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:13:07,278 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:13:08,519 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:13:09,862 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:13:11,185 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:16:08,148 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:16:08,919 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:16:10,405 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:16:11,653 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:16:11,995 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:16:13,196 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:16:14,710 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:16:16,179 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:16:18,101 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:16:19,384 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:16:20,730 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:16:22,051 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:00,230 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:02,119 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:03,949 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:05,796 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:07,604 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:10,736 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:13,445 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:16,191 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:18,901 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:21,314 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:23,287 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:25,209 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:27,147 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:29,123 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:31,076 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:33,048 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:35,258 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:37,281 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:39,378 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:41,346 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:43,309 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:46,289 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:49,315 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:52,350 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:55,389 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:57,337 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:17:59,260 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:01,194 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:03,145 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:05,058 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:06,967 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:08,875 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:10,838 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:12,933 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:14,978 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:17,037 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:19,103 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:22,381 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:25,533 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:28,605 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:31,732 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:33,783 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:35,779 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:37,751 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:39,710 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:41,660 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:43,608 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:18:45,613 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:08,963 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:12,156 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:15,105 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:18,044 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:20,971 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:23,997 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:26,980 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:30,008 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:33,080 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:35,154 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:36,985 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:38,812 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:41,566 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:43,643 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:45,916 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:48,103 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:50,376 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:53,851 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:19:57,284 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:20:00,773 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:20:04,294 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:20:07,978 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:20:11,497 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:20:14,967 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:21:23,802 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:21:26,337 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:21:28,946 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:21:31,449 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:21:34,042 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:21:37,872 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:21:41,799 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:21:45,621 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:21:49,476 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:21:53,118 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:21:56,784 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:00,537 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:04,183 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:09,144 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:13,811 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:18,582 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:23,299 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:24,426 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:25,517 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:26,590 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:27,656 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:28,723 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:29,799 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:30,928 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:31,993 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:33,009 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:34,066 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:35,072 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:36,119 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:37,227 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:38,294 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:39,331 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:40,383 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:41,494 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:42,674 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:43,771 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:44,899 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:46,108 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:47,264 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:48,397 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:49,549 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:50,613 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:51,682 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:52,729 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:53,781 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:54,888 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:55,946 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:57,017 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:22:58,109 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:23:00,423 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:23:02,641 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:23:04,845 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:23:07,174 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:23:11,268 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:23:14,784 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:23:18,312 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:23:31,170 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:23:33,268 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:23:35,409 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:23:37,480 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:27:12,912 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:27:14,121 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:27:14,678 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:27:15,240 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:27:15,749 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:27:16,773 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:27:17,363 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:27:18,449 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:27:18,934 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:27:19,379 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:27:19,797 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:27:21,888 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:29:41,892 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:29:46,254 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:29:54,322 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:12,922 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:14,887 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:16,663 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:18,507 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:20,146 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:21,949 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:23,586 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:25,288 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:26,852 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:28,657 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:30,253 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:31,983 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:30:33,065 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:35:37,619 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:36:19,393 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:36:21,645 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted -! 12/9/25 01:47:26:599 warning: Ice.ThreadPool.Client-0: dispatch exception: identity: Q)\\U\'tZ+SY4sU_\\}\'afy/b87e609e-445c-40ef-af9a-2f323303229d facet: operation: finished remote host: 127.0.0.1 remote port: 14064 java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0 at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64) at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70) at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248) at java.base/java.util.Objects.checkIndex(Objects.java:374) at java.base/java.util.ArrayList.remove(ArrayList.java:536) at ome.xml.model.ReferenceList.remove(ReferenceList.java:102) at ome.xml.model.ReferenceList.set(ReferenceList.java:129) at ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341) at ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003) at ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426) at ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100) at loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924) at loci.formats.in.OMEXMLReader.initFile(OMEXMLReader.java:331) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=Index 1 out of bounds for length 0} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 01:49:03,267 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted -! 12/9/25 01:49:27:298 warning: Ice.ThreadPool.Client-0: dispatch exception: identity: ecLp2o`=\'pBYF5nezF_a/525eb529-3fbc-4b01-950d-41d56bc4a41b facet: operation: finished remote host: 127.0.0.1 remote port: 14064 java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0 at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64) at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70) at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248) at java.base/java.util.Objects.checkIndex(Objects.java:374) at java.base/java.util.ArrayList.remove(ArrayList.java:536) at ome.xml.model.ReferenceList.remove(ReferenceList.java:102) at ome.xml.model.ReferenceList.set(ReferenceList.java:129) at ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341) at ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003) at ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426) at ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100) at loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924) at loci.formats.in.OMEXMLReader.initFile(OMEXMLReader.java:331) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=Index 1 out of bounds for length 0} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 01:50:19,411 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:23,460 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:27,281 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:30,978 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:34,045 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:37,024 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:39,950 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:42,869 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:45,809 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:47,322 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:48,817 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:50,360 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:52,530 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:55,274 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:50:58,111 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:00,880 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:02,983 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:05,068 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:07,153 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:09,272 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:11,382 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:12,727 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:14,082 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:15,419 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:17,425 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:21,042 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:24,836 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted -! 12/9/25 01:51:27:309 warning: Ice.ThreadPool.Client-0: dispatch exception: identity: =ZDL54\";JJOj,_vhxI:V/52b0d646-604a-4c66-8c0d-854c6106ea42 facet: operation: finished remote host: 127.0.0.1 remote port: 14064 java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0 at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64) at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70) at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248) at java.base/java.util.Objects.checkIndex(Objects.java:374) at java.base/java.util.ArrayList.remove(ArrayList.java:536) at ome.xml.model.ReferenceList.remove(ReferenceList.java:102) at ome.xml.model.ReferenceList.set(ReferenceList.java:129) at ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341) at ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003) at ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426) at ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100) at loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924) at loci.formats.in.OMEXMLReader.initFile(OMEXMLReader.java:331) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=Index 1 out of bounds for length 0} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 01:51:28,495 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:32,116 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:34,120 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:35,621 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:38,710 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:41,704 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:44,784 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:47,766 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:49,261 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:50,754 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:51:52,227 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:52:26,326 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted Could not login with command line arguments.Glacier2.PermissionDeniedException reason = "Password check failed for '537a5eb4-248d-4762-a843-a4288e10ffde': [id=3014]" at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.lang.Class.newInstance(Class.java:584) at IceInternal.BasicStream.createUserException(BasicStream.java:2785) at IceInternal.BasicStream.access$300(BasicStream.java:14) at IceInternal.BasicStream$EncapsDecoder11.throwException(BasicStream.java:3620) at IceInternal.BasicStream.throwException(BasicStream.java:2291) at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399) at Glacier2.RouterPrxHelper.end_createSession(RouterPrxHelper.java:178) at Glacier2.RouterPrxHelper.createSession(RouterPrxHelper.java:49) at Glacier2.RouterPrxHelper.createSession(RouterPrxHelper.java:41) at omero.client.createSession(client.java:776) at omero.client.createSession(client.java:719) at omero.gateway.Gateway.createSession(Gateway.java:1045) at omero.gateway.Gateway.connect(Gateway.java:297) at integration.gateway.GatewayUsageTest.testLoginFallback(GatewayUsageTest.java:154) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:135) at org.testng.internal.invokers.InvokeMethodRunnable.runOne(InvokeMethodRunnable.java:44) at org.testng.internal.invokers.InvokeMethodRunnable.call(InvokeMethodRunnable.java:72) at org.testng.internal.invokers.InvokeMethodRunnable.call(InvokeMethodRunnable.java:10) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Could not login with command line arguments.Glacier2.PermissionDeniedException reason = "Password check failed for '537a5eb4-248d-4762-a843-a4288e10ffde': [id=3014]" at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.lang.Class.newInstance(Class.java:584) at IceInternal.BasicStream.createUserException(BasicStream.java:2785) at IceInternal.BasicStream.access$300(BasicStream.java:14) at IceInternal.BasicStream$EncapsDecoder11.throwException(BasicStream.java:3620) at IceInternal.BasicStream.throwException(BasicStream.java:2291) at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399) at Glacier2.RouterPrxHelper.end_createSession(RouterPrxHelper.java:178) at Glacier2.RouterPrxHelper.createSession(RouterPrxHelper.java:49) at Glacier2.RouterPrxHelper.createSession(RouterPrxHelper.java:41) at omero.client.createSession(client.java:776) at omero.client.createSession(client.java:719) at omero.gateway.Gateway.createSession(Gateway.java:1045) at omero.gateway.Gateway.connect(Gateway.java:297) at integration.gateway.GatewayUsageTest.testLoginFallback(GatewayUsageTest.java:154) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:135) at org.testng.internal.invokers.InvokeMethodRunnable.runOne(InvokeMethodRunnable.java:44) at org.testng.internal.invokers.InvokeMethodRunnable.call(InvokeMethodRunnable.java:72) at org.testng.internal.invokers.InvokeMethodRunnable.call(InvokeMethodRunnable.java:10) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Exception in thread "TestNG-method=testLoginFallback-1" Support for FileAnnotationData is deprecated. Use OriginalFile instead. Could not load table dataomero.IllegalArgumentException: start value can't be greater than stop value at omero.gateway.facility.TablesFacility.query(TablesFacility.java:320) at integration.gateway.TablesFacilityTest.testInvalidParams(TablesFacilityTest.java:220) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:135) at org.testng.internal.invokers.InvokeMethodRunnable.runOne(InvokeMethodRunnable.java:44) at org.testng.internal.invokers.InvokeMethodRunnable.call(InvokeMethodRunnable.java:72) at org.testng.internal.invokers.InvokeMethodRunnable.call(InvokeMethodRunnable.java:10) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Could not load table dataomero.IllegalArgumentException: start value can't be greater than stop value at omero.gateway.facility.TablesFacility.query(TablesFacility.java:320) at integration.gateway.TablesFacilityTest.testInvalidParams(TablesFacilityTest.java:220) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:135) at org.testng.internal.invokers.InvokeMethodRunnable.runOne(InvokeMethodRunnable.java:44) at org.testng.internal.invokers.InvokeMethodRunnable.call(InvokeMethodRunnable.java:72) at org.testng.internal.invokers.InvokeMethodRunnable.call(InvokeMethodRunnable.java:10) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Exception in thread "TestNG-method=testInvalidParams-1" Could not load table dataomero.IllegalArgumentException: step value is greater than the specified range at omero.gateway.facility.TablesFacility.query(TablesFacility.java:324) at integration.gateway.TablesFacilityTest.testInvalidParams(TablesFacilityTest.java:229) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:135) at org.testng.internal.invokers.InvokeMethodRunnable.runOne(InvokeMethodRunnable.java:44) at org.testng.internal.invokers.InvokeMethodRunnable.call(InvokeMethodRunnable.java:72) at org.testng.internal.invokers.InvokeMethodRunnable.call(InvokeMethodRunnable.java:10) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Could not load table dataomero.IllegalArgumentException: step value is greater than the specified range at omero.gateway.facility.TablesFacility.query(TablesFacility.java:324) at integration.gateway.TablesFacilityTest.testInvalidParams(TablesFacilityTest.java:229) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:135) at org.testng.internal.invokers.InvokeMethodRunnable.runOne(InvokeMethodRunnable.java:44) at org.testng.internal.invokers.InvokeMethodRunnable.call(InvokeMethodRunnable.java:72) at org.testng.internal.invokers.InvokeMethodRunnable.call(InvokeMethodRunnable.java:10) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Exception in thread "TestNG-method=testInvalidParams-1" No concrete type specified for column 'column1', using Object.toString() Request rows 1545 to 1555; columns [2] Request rows 941 to 1020; columns [4, 10] Request rows 1891 to 1939; columns [9, 10, 7, 2] Request rows 1813 to 1881; columns [3] Request rows 1787 to 1809; columns [10, 9, 7] 2025-12-09 01:54:27,067 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:56:27,085 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:58:38,078 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:16,069 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:26,260 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:27,510 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:30,043 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:31,259 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:32,532 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:34,511 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:35,734 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:36,904 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:38,164 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:40,516 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:41,261 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:42,438 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:43,225 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:44,393 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:45,150 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:46,343 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:47,134 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:48,353 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:49,114 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:50,327 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:51,137 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:52,358 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:53,104 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:54,273 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:55,028 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:56,343 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:57,072 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:58,318 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 01:59:59,081 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:00,398 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:01,181 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:02,561 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:03,293 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:04,579 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:05,325 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:06,600 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:07,351 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:08,604 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:09,391 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:10,774 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:11,534 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:15,919 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:16,685 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:22,886 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:23,688 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:26,906 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:27,656 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:30,836 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:31,583 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:34,723 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:35,469 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:38,668 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:39,411 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:42,531 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:43,274 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:46,584 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:47,338 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:50,661 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:51,418 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:54,696 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:55,447 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:58,748 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:00:59,498 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:02,848 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:03,628 ERROR [ o.formats.importer.util.ClientKeepAlive] (9-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:11,097 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:11,840 ERROR [ o.formats.importer.util.ClientKeepAlive] (2-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:18,292 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:19,034 ERROR [ o.formats.importer.util.ClientKeepAlive] (5-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:22,490 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:23,274 ERROR [ o.formats.importer.util.ClientKeepAlive] (8-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:26,427 ERROR [ o.formats.importer.util.ClientKeepAlive] (0-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:27,225 ERROR [ o.formats.importer.util.ClientKeepAlive] (1-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:30,383 ERROR [ o.formats.importer.util.ClientKeepAlive] (3-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:31,177 ERROR [ o.formats.importer.util.ClientKeepAlive] (4-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted =============================================== OmeroJava.integration Total tests run: 2589, Passes: 2579, Failures: 10, Skips: 0 =============================================== 2025-12-09 02:01:34,410 ERROR [ o.formats.importer.util.ClientKeepAlive] (6-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted 2025-12-09 02:01:35,193 ERROR [ o.formats.importer.util.ClientKeepAlive] (7-thread-1) Exception while executing ping(), logging Connector out: java.lang.RuntimeException: Ice.CommunicatorDestroyedException at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:845) at ome.formats.importer.util.ClientKeepAlive.run(ClientKeepAlive.java:77) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.CommunicatorDestroyedException: null at IceInternal.Instance.proxyFactory(Instance.java:239) at IceInternal.BasicStream.writeProxy(BasicStream.java:2142) at omero.api.ServiceInterfacePrxHelper.__write(ServiceInterfacePrxHelper.java:114) at omero.api.ServiceListHelper.write(ServiceListHelper.java:37) at omero.api.ServiceFactoryPrxHelper.begin_keepAllAlive(ServiceFactoryPrxHelper.java:5946) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5846) at omero.api.ServiceFactoryPrxHelper.keepAllAlive(ServiceFactoryPrxHelper.java:5833) at ome.formats.OMEROMetadataStoreClient.ping(OMEROMetadataStoreClient.java:838) ... 7 common frames omitted The tests failed. BUILD SUCCESSFUL Total time: 67 minutes 37 seconds + /home/omero/workspace/OMERO-test-integration/src/build.py -f components/tools/OmeroPy/build.xml integration -Dtestreports.dir=target/reports/integration Buildfile: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/build.xml Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy... Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy... python-integration: Created dir: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/target/reports/integration ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-9.0.2, pluggy-1.6.0 -- /home/omero/workspace/OMERO-test-integration/.venv3/bin/python3.11 cachedir: .pytest_cache django: version: 5.2.9, settings: omeroweb.settings (from ini) rootdir: /home/omero/workspace/OMERO-test-integration/src/components/tools configfile: pytest.ini plugins: xdist-3.8.0, mock-3.15.1, django-4.11.1 collecting ... collected 2044 items / 36 deselected / 2008 selected test/integration/clitest/test_admin.py::TestAdmin::test_checkupgrade0 PASSED [ 0%] test/integration/clitest/test_admin.py::TestAdmin::test_checkupgrade1 PASSED [ 0%] test/integration/clitest/test_admin.py::TestAdmin::test_log PASSED [ 0%] test/integration/clitest/test_admin.py::TestAdminRestrictedAdmin::test_log PASSED [ 0%] test/integration/clitest/test_admin.py::TestAdminRestrictedAdmin::test_checkupgrade0 PASSED [ 0%] test/integration/clitest/test_admin.py::TestAdminRestrictedAdmin::test_checkupgrade1 PASSED [ 0%] test/integration/clitest/test_chgrp.py::TestChgrp::testChgrpMyData[-rw-----Image] PASSED [ 0%] test/integration/clitest/test_chgrp.py::TestChgrp::testChgrpMyData[-rw-----Dataset] PASSED [ 0%] test/integration/clitest/test_chgrp.py::TestChgrp::testChgrpMyData[-rw-----Project] PASSED [ 0%] test/integration/clitest/test_chgrp.py::TestChgrp::testChgrpMyData[-rw-----Plate] PASSED [ 0%] test/integration/clitest/test_chgrp.py::TestChgrp::testChgrpMyData[-rw-----Screen] PASSED [ 0%] test/integration/clitest/test_chgrp.py::TestChgrp::testChgrpMyData[-rwr----Image] PASSED [ 0%] test/integration/clitest/test_chgrp.py::TestChgrp::testChgrpMyData[-rwr----Dataset] PASSED [ 0%] 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test/integration/clitest/test_chown.py::TestChown::testMultipleSkipheadsPlusObjectsSeparated[True-2] PASSED [ 8%] test/integration/clitest/test_chown.py::TestChown::testMultipleSkipheadsPlusObjectsSeparated[True-3] PASSED [ 8%] test/integration/clitest/test_chown.py::TestChown::testMultipleSkipheadsPlusObjectsSeparated[False-1] PASSED [ 8%] test/integration/clitest/test_chown.py::TestChown::testMultipleSkipheadsPlusObjectsSeparated[False-2] PASSED [ 8%] test/integration/clitest/test_chown.py::TestChown::testMultipleSkipheadsPlusObjectsSeparated[False-3] PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testMultipleSkipheadsPlusObjectsInterlaced[True-1] PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testMultipleSkipheadsPlusObjectsInterlaced[True-2] PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testMultipleSkipheadsPlusObjectsInterlaced[True-3] PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testMultipleSkipheadsPlusObjectsInterlaced[False-1] PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testMultipleSkipheadsPlusObjectsInterlaced[False-2] PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testMultipleSkipheadsPlusObjectsInterlaced[False-3] PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testDryRun PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testExcludeNone PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testExcludeDataset PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testExcludeImage PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testExcludeOverridesInclude PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testSeparateAnnotationTransfer PASSED [ 9%] test/integration/clitest/test_chown.py::TestChown::testOutputWithElision PASSED [ 9%] test/integration/clitest/test_chown.py::TestTagChown::testChownOneTagSetWithUniqueTags PASSED [ 9%] test/integration/clitest/test_chown.py::TestChownRoot::testChownBasicUsageWithId PASSED [ 9%] test/integration/clitest/test_chown.py::TestChownNonGroupOwner::testChownBasicUsageWithId PASSED [ 9%] test/integration/clitest/test_cleanse.py::TestCleanse::testCleanseAdminOnly PASSED [ 9%] test/integration/clitest/test_cleanse.py::TestCleanseFullAdmin::testCleanseBasic PASSED [ 9%] test/integration/clitest/test_cleanse.py::TestCleanseFullAdmin::testCleanseNonsenseName PASSED [ 9%] test/integration/clitest/test_cleanse.py::TestCleanseRestrictedAdmin::test_cleanse_restricted_admin PASSED [ 10%] test/integration/clitest/test_cleanse.py::TestFixPyramids::test_fixpyramids_admin_only PASSED [ 10%] test/integration/clitest/test_cleanse.py::TestFixPyramidsRestrictedAdmin::test_fixpyramids_restricted_admin PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testBadVersionDies PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPasswordIsAskedForAgainIfDiffer PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPasswordIsAskedForAgainIfEmpty PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPassword[--] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPassword[----no-salt] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPassword[-0-] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPassword[-0---no-salt] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPassword[-1-] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPassword[-1---no-salt] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPassword[ome--] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPassword[ome----no-salt] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPassword[ome-0-] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPassword[ome-0---no-salt] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPassword[ome-1-] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testPassword[ome-1---no-salt] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testScript[--] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testScript[---f] PASSED [ 10%] test/integration/clitest/test_db.py::TestDatabase::testScript[----file] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScript[---no-salt-] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScript[---no-salt--f] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScript[---no-salt---file] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScript[--password ome--] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScript[--password ome---f] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScript[--password ome----file] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScript[--password ome---no-salt-] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScript[--password ome---no-salt--f] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScript[--password ome---no-salt---file] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScriptDeveloperArgs[%s %s %s--] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScriptDeveloperArgs[%s %s %s---f] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScriptDeveloperArgs[%s %s %s----file] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScriptDeveloperArgs[%s %s %s---no-salt-] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScriptDeveloperArgs[%s %s %s---no-salt--f] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScriptDeveloperArgs[%s %s %s---no-salt---file] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScriptDeveloperArgs[--version %s --patch %s --password %s--] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScriptDeveloperArgs[--version %s --patch %s --password %s---f] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScriptDeveloperArgs[--version %s --patch %s --password %s----file] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScriptDeveloperArgs[--version %s --patch %s --password %s---no-salt-] PASSED [ 11%] test/integration/clitest/test_db.py::TestDatabase::testScriptDeveloperArgs[--version %s --patch %s --password %s---no-salt--f] PASSED [ 12%] test/integration/clitest/test_db.py::TestDatabase::testScriptDeveloperArgs[--version %s --patch %s --password %s---no-salt---file] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testDeleteMyData[Image-] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testDeleteMyData[Image-I] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testDeleteMyData[Dataset-] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testDeleteMyData[Dataset-I] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testDeleteMyData[Project-] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testDeleteMyData[Project-I] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testDeleteMyData[Plate-] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testDeleteMyData[Plate-I] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testDeleteMyData[Screen-] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testDeleteMyData[Screen-I] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testFileset[image-1] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testFileset[image-2] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testFileset[fileset-1] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testFileset[fileset-2] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testFilesetPartialFailing PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testFilesetAllImagesDeleteDataset PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsSameClass[True-1] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsSameClass[True-2] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsSameClass[True-3] PASSED [ 12%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsSameClass[False-1] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsSameClass[False-2] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsSameClass[False-3] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsTwoClassesSeparated[True-1] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsTwoClassesSeparated[True-2] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsTwoClassesSeparated[True-3] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsTwoClassesSeparated[False-1] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsTwoClassesSeparated[False-2] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsTwoClassesSeparated[False-3] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsTwoClassesInterlaced[True-1] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsTwoClassesInterlaced[True-2] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsTwoClassesInterlaced[True-3] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsTwoClassesInterlaced[False-1] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsTwoClassesInterlaced[False-2] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSimpleObjectsTwoClassesInterlaced[False-3] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testBasicSkipheadBothForms[True-1-/Dataset] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testBasicSkipheadBothForms[True-1-] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testBasicSkipheadBothForms[True-2-/Dataset] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testBasicSkipheadBothForms[True-2-] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testBasicSkipheadBothForms[False-1-/Dataset] PASSED [ 13%] test/integration/clitest/test_delete.py::TestDelete::testBasicSkipheadBothForms[False-1-] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testBasicSkipheadBothForms[False-2-/Dataset] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testBasicSkipheadBothForms[False-2-] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsSameClass[True-1] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsSameClass[True-2] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsSameClass[True-3] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsSameClass[False-1] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsSameClass[False-2] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsSameClass[False-3] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsPlusObjectsSeparated[True-1] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsPlusObjectsSeparated[True-2] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsPlusObjectsSeparated[True-3] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsPlusObjectsSeparated[False-1] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsPlusObjectsSeparated[False-2] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsPlusObjectsSeparated[False-3] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsPlusObjectsInterlaced[True-1] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsPlusObjectsInterlaced[True-2] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsPlusObjectsInterlaced[True-3] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsPlusObjectsInterlaced[False-1] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsPlusObjectsInterlaced[False-2] PASSED [ 14%] test/integration/clitest/test_delete.py::TestDelete::testMultipleSkipheadsPlusObjectsInterlaced[False-3] PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testDryRun PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testExcludeNone PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testExcludeDataset PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testExcludeImage PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testExcludeOverridesInclude PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testDefaultExclusion PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testDefaultExclusionOverride PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testDefaultExclusionPartialOverride PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testSeparateAnnotationDelete PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testLinkedAnnotationDelete PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testLinkedAnnotationDeleteWithOverride PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testInputWithElisionDefault[1] PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testInputWithElisionDefault[2] PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testInputWithElisionDefault[3] PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testInputWithElisionForce PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testElisionDefaultFailForce PASSED [ 15%] test/integration/clitest/test_delete.py::TestDelete::testOutputWithElision PASSED [ 15%] test/integration/clitest/test_delete.py::TestTagDelete::testDeleteOneTagSetNotTags PASSED [ 15%] test/integration/clitest/test_delete.py::TestTagDelete::testDeleteTwoTagSetsNotTags PASSED [ 15%] test/integration/clitest/test_delete.py::TestTagDelete::testDeleteOneTagSetIncludingTags PASSED [ 16%] test/integration/clitest/test_delete.py::TestTagDelete::testDeleteTwoTagSetsIncludingTags PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testNonExistingOriginalFile[] PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testNonExistingOriginalFile[OriginalFile:] PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testOriginalFileTmpfile[] PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testOriginalFileTmpfile[OriginalFile:] PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testOriginalFileStdout[] PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testOriginalFileStdout[OriginalFile:] PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testOriginalFileMultipleGroups[] PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testOriginalFileMultipleGroups[OriginalFile:] PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testNonExistingFileAnnotation PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testFileAnnotationTmpfile PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testFileAnnotationStdout PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testFileAnnotationMultipleGroups PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testNonExistingImage PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testImageFileset[True] PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testImageFileset[False] PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testSingleImageWithCompanion PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testMIF PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testImageNoFileset PASSED [ 16%] test/integration/clitest/test_download.py::TestDownload::testImageMultipleGroups PASSED [ 17%] test/integration/clitest/test_download.py::TestDownload::testValidPolicy PASSED [ 17%] test/integration/clitest/test_download.py::TestDownload::testPolicyGlobalRestriction[+read,+write,+image] FAILED [ 17%] test/integration/clitest/test_download.py::TestDownload::testPolicyGlobalRestriction[-read,-write,-image,-plate] SKIPPED [ 17%] test/integration/clitest/test_download.py::TestDownload::testPolicyGlobalRestriction[-read,+write,+image,-plate] SKIPPED [ 17%] test/integration/clitest/test_download.py::TestDownload::testPolicyGlobalRestriction[+read,+write,+image,-plate] SKIPPED [ 17%] test/integration/clitest/test_download.py::TestDownload::testPolicyGlobalRestriction[+read,+write,+image,+plate] SKIPPED [ 17%] test/integration/clitest/test_download.py::TestDownload::testPolicyGroupRestriction[+read,+write,+image] FAILED [ 17%] test/integration/clitest/test_download.py::TestDownload::testPolicyGroupRestriction[-read,-write,-image,-plate] FAILED [ 17%] test/integration/clitest/test_download.py::TestDownload::testPolicyGroupRestriction[-read,+write,+image,-plate] FAILED [ 17%] test/integration/clitest/test_download.py::TestDownload::testPolicyGroupRestriction[+read,+write,+image,-plate] FAILED [ 17%] test/integration/clitest/test_download.py::TestDownload::testPolicyGroupRestriction[+read,+write,+image,+plate] FAILED [ 17%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObject[Image-] PASSED [ 17%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObject[Image-I] PASSED [ 17%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObject[Dataset-] PASSED [ 17%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObject[Dataset-I] PASSED [ 17%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObject[Project-] PASSED [ 17%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObject[Project-I] PASSED [ 17%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObject[Plate-] PASSED [ 17%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObject[Plate-I] PASSED [ 17%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObject[Screen-] PASSED [ 18%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObject[Screen-I] PASSED [ 18%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObjectDryRun PASSED [ 18%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObjectReport PASSED [ 18%] test/integration/clitest/test_duplicate.py::TestDuplicate::testDuplicateSingleObjectDryRunReport PASSED [ 18%] test/integration/clitest/test_duplicate.py::TestDuplicate::testBasicHierarchyDuplication PASSED [ 18%] test/integration/clitest/test_duplicate.py::TestDuplicate::testIgnoreLinks PASSED [ 18%] test/integration/clitest/test_duplicate.py::TestDuplicate::testIgnoreLinksOverridden PASSED [ 18%] test/integration/clitest/test_duplicate.py::TestDuplicate::testReferencing PASSED [ 18%] test/integration/clitest/test_duplicate.py::TestDuplicate::testSkipheadDuplication PASSED [ 18%] test/integration/clitest/test_fs.py::TestFS::testRepos PASSED [ 18%] test/integration/clitest/test_fs.py::TestFS::testSetsWithTransfer PASSED [ 18%] test/integration/clitest/test_fs.py::TestFS::testSetsAdminOnly PASSED [ 18%] test/integration/clitest/test_fs.py::TestFS::testMkdirAdminOnly PASSED [ 18%] test/integration/clitest/test_fs.py::TestFS::testImportTime[all-True] FAILED [ 18%] test/integration/clitest/test_fs.py::TestFS::testImportTime[all-False] PASSED [ 18%] test/integration/clitest/test_fs.py::TestFS::testImportTime[minmax-True] FAILED [ 18%] test/integration/clitest/test_fs.py::TestFS::testImportTime[minmax-False] PASSED [ 18%] test/integration/clitest/test_fs.py::TestFS::testImportTime[thumbnails-True] FAILED [ 18%] test/integration/clitest/test_fs.py::TestFS::testImportTime[thumbnails-False] PASSED [ 18%] test/integration/clitest/test_fs.py::TestFsRoot::testMkdirAsAdminSimpleDirCreation PASSED [ 19%] test/integration/clitest/test_fs.py::TestFsRoot::testMkdirAsAdminHierarchyOnlyPreexisting PASSED [ 19%] test/integration/clitest/test_fs.py::TestFsRoot::testMkdirAsAdminHierarchyParents PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testList[None-None] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testList[None-id] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testList[None-name] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testList[count-None] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testList[count-id] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testList[count-name] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testList[long-None] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testList[long-id] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testList[long-name] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testAddAdminOnly PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testInfoNoArgument PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testInfoArgument[id] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testInfoArgument[name] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testInfoArgument[--group-id] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testInfoArgument[--group-name] PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testInfoInvalidGroup PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testListUsersNoArgument PASSED [ 19%] test/integration/clitest/test_group.py::TestGroup::testListUsersArgument[id] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroup::testListUsersArgument[name] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroup::testListUsersArgument[--group-id] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroup::testListUsersArgument[--group-name] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroup::testListUsersInvalidArgument PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testAddDefaults PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testAddPerms[--perms-rw----] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testAddPerms[--perms-rwr---] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testAddPerms[--perms-rwra--] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testAddPerms[--perms-rwrw--] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testAddPerms[--type-private] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testAddPerms[--type-read-only] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testAddPerms[--type-read-annotate] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testAddPerms[--type-read-write] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testAddSameNamefails PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testAddIgnoreExisting PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rw-----rw-------id] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rw-----rw-------name] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rw-----rwr------id] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rw-----rwr------name] PASSED [ 20%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rw-----rwra-----id] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rw-----rwra-----name] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rw-----rwrw-----id] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rw-----rwrw-----name] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwr----rw-------id] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwr----rw-------name] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwr----rwr------id] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwr----rwr------name] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwr----rwra-----id] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwr----rwra-----name] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwr----rwrw-----id] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwr----rwrw-----name] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwra---rw-------id] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwra---rw-------name] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwra---rwr------id] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwra---rwr------name] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwra---rwra-----id] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwra---rwra-----name] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwra---rwrw-----id] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwra---rwrw-----name] PASSED [ 21%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwrw---rw-------id] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwrw---rw-------name] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwrw---rwr------id] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwrw---rwr------name] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwrw---rwra-----id] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwrw---rwra-----name] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwrw---rwrw-----id] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--perms-rwrw---rwrw-----name] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-private-rw-------id] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-private-rw-------name] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-private-rwr------id] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-private-rwr------name] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-private-rwra-----id] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-private-rwra-----name] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-private-rwrw-----id] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-private-rwrw-----name] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-only-rw-------id] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-only-rw-------name] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-only-rwr------id] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-only-rwr------name] PASSED [ 22%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-only-rwra-----id] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-only-rwra-----name] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-only-rwrw-----id] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-only-rwrw-----name] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-annotate-rw-------id] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-annotate-rw-------name] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-annotate-rwr------id] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-annotate-rwr------name] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-annotate-rwra-----id] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-annotate-rwra-----name] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-annotate-rwrw-----id] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-annotate-rwrw-----name] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-write-rw-------id] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-write-rw-------name] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-write-rwr------id] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-write-rwr------name] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-write-rwra-----id] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-write-rwra-----name] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-write-rwrw-----id] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testPerms[--type-read-write-rwrw-----name] PASSED [ 23%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[None-id---id] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[None-id---name] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[None-omeName---id] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[None-omeName---name] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[None---user-id---id] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[None---user-id---name] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[None---user-name---id] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[None---user-name---name] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[--as-owner-id---id] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[--as-owner-id---name] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[--as-owner-omeName---id] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[--as-owner-omeName---name] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[--as-owner---user-id---id] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[--as-owner---user-id---name] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[--as-owner---user-name---id] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testAddUser[--as-owner---user-name---name] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-True-id---id] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-True-id---name] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-True-omeName---id] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-True-omeName---name] PASSED [ 24%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-True---user-id---id] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-True---user-id---name] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-True---user-name---id] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-True---user-name---name] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-False-id---id] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-False-id---name] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-False-omeName---id] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-False-omeName---name] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-False---user-id---id] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-False---user-id---name] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-False---user-name---id] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[None-False---user-name---name] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-True-id---id] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-True-id---name] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-True-omeName---id] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-True-omeName---name] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-True---user-id---id] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-True---user-id---name] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-True---user-name---id] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-True---user-name---name] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-False-id---id] PASSED [ 25%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-False-id---name] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-False-omeName---id] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-False-omeName---name] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-False---user-id---id] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-False---user-id---name] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-False---user-name---id] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testRemoveUser[--as-owner-False---user-name---name] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testCopyUsers[None-id-id] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testCopyUsers[None-id-name] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testCopyUsers[None-name-id] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testCopyUsers[None-name-name] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testCopyUsers[--as-owner-id-id] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testCopyUsers[--as-owner-id-name] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testCopyUsers[--as-owner-name-id] PASSED [ 26%] test/integration/clitest/test_group.py::TestGroupRoot::testCopyUsers[--as-owner-name-name] PASSED [ 26%] test/integration/clitest/test_import.py::TestImport::testAutoClose PASSED [ 26%] test/integration/clitest/test_import.py::TestImport::testChecksumAlgorithm[Adler-32-legacy] PASSED [ 26%] test/integration/clitest/test_import.py::TestImport::testChecksumAlgorithm[Adler-32-underscore] PASSED [ 26%] test/integration/clitest/test_import.py::TestImport::testChecksumAlgorithm[CRC-32-underscore] PASSED [ 26%] test/integration/clitest/test_import.py::TestImport::testChecksumAlgorithm[File-Size-64-underscore] PASSED [ 26%] test/integration/clitest/test_import.py::TestImport::testChecksumAlgorithm[MD5-128-underscore] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testChecksumAlgorithm[Murmur3-32-underscore] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testChecksumAlgorithm[Murmur3-128-underscore] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testChecksumAlgorithm[SHA1-160-underscore] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText[Python-1-Official-True] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText[Python-1-Official-False] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText[Python-1-Deprecated-True] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText[Python-1-Deprecated-False] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText[Java-1-Official-True] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText[Java-1-Official-False] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText[Java-1-Deprecated-True] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText[Java-1-Deprecated-False] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText[Java-2-Official-True] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText[Java-2-Official-False] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText[Java-2-Deprecated-True] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText[Java-2-Deprecated-False] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText_one_ns[Python-1-Official] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText_one_ns[Python-1-Deprecated] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText_one_ns[Java-1-Official] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText_one_ns[Java-1-Deprecated] PASSED [ 27%] test/integration/clitest/test_import.py::TestImport::testAnnotationText_one_ns[Java-2-Official] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testAnnotationText_one_ns[Java-2-Deprecated] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testAnnotationLink[Python-1-Official] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testAnnotationLink[Python-1-Deprecated] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testAnnotationLink[Java-1-Official] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testAnnotationLink[Java-1-Deprecated] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testAnnotationLink[Java-2-Official] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testAnnotationLink[Java-2-Deprecated] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testTargetArgument[source0-True] FAILED [ 28%] test/integration/clitest/test_import.py::TestImport::testTargetArgument[source0-False] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testTargetArgument[source1-True] FAILED [ 28%] test/integration/clitest/test_import.py::TestImport::testTargetArgument[source1-False] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testTargetArgument[source2-True] FAILED [ 28%] test/integration/clitest/test_import.py::TestImport::testTargetArgument[source2-False] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testTargetArgument[source3-True] FAILED [ 28%] test/integration/clitest/test_import.py::TestImport::testTargetArgument[source3-False] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testTargetArgument[source4-True] FAILED [ 28%] test/integration/clitest/test_import.py::TestImport::testTargetArgument[source4-False] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testTargetArgument[source5-True] FAILED [ 28%] test/integration/clitest/test_import.py::TestImport::testTargetArgument[source5-False] PASSED [ 28%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[-True] FAILED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[-False] PASSED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[+-True] FAILED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[+-False] PASSED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[--True] FAILED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[--False] PASSED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[%-True] FAILED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[%-False] PASSED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[@-True] FAILED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[@-False] PASSED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[-True] FAILED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[-False] PASSED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[+-True] FAILED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[+-False] PASSED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[--True] FAILED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[--False] PASSED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[%-True] FAILED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[%-False] PASSED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[@-True] FAILED [ 29%] test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[@-False] PASSED [ 29%] test/integration/clitest/test_import.py::TestImport::testMultipleNameModelTargets[-True] FAILED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameModelTargets[-False] PASSED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameModelTargets[+-True] FAILED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameModelTargets[+-False] PASSED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameModelTargets[--True] FAILED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameModelTargets[--False] PASSED [ 30%] test/integration/clitest/test_import.py::TestImport::testUniqueMultipleNameModelTargets[True] PASSED [ 30%] test/integration/clitest/test_import.py::TestImport::testUniqueMultipleNameModelTargets[False] PASSED [ 30%] test/integration/clitest/test_import.py::TestImport::testNestedNameTemplateTargetArgument[True] FAILED [ 30%] test/integration/clitest/test_import.py::TestImport::testNestedNameTemplateTargetArgument[False] PASSED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameTemplateTargetArgument[-True] FAILED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameTemplateTargetArgument[-False] PASSED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameTemplateTargetArgument[+-True] FAILED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameTemplateTargetArgument[+-False] PASSED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameTemplateTargetArgument[--True] FAILED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameTemplateTargetArgument[--False] PASSED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameTemplateTargetArgument[@-True] FAILED [ 30%] test/integration/clitest/test_import.py::TestImport::testMultipleNameTemplateTargetArgument[@-False] PASSED [ 30%] test/integration/clitest/test_import.py::TestImport::testUniqueMultipleNameTemplateTargetArgument[True] FAILED [ 30%] test/integration/clitest/test_import.py::TestImport::testUniqueMultipleNameTemplateTargetArgument[False] PASSED [ 30%] test/integration/clitest/test_import.py::TestImport::testImportLinkableTarget[False-False] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testImportLinkableTarget[False-True] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testImportLinkableTarget[True-False] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testImportLinkableTarget[True-True] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testBadTargetArgument[Project] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testBadTargetArgument[Plate] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testBadTargetArgument[Image] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testBadModelTargetDiscriminator[Dataset] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testBadModelTargetDiscriminator[Screen] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testDebugArgument[None-ALL] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testDebugArgument[None-TRACE] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testDebugArgument[None-DEBUG] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testDebugArgument[None-INFO] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testDebugArgument[None-WARN] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testDebugArgument[None-ERROR] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testDebugArgument[---ALL] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testDebugArgument[---TRACE] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testDebugArgument[---DEBUG] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testDebugArgument[---INFO] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testDebugArgument[---WARN] PASSED [ 31%] test/integration/clitest/test_import.py::TestImport::testDebugArgument[---ERROR] PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testImportOutputDefault PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testImportOutputYaml PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testImportOutputLegacy PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testImportOutputDefaultWithScreen[1] FAILED [ 32%] test/integration/clitest/test_import.py::TestImport::testImportOutputDefaultWithScreen[2] FAILED [ 32%] test/integration/clitest/test_import.py::TestImport::testImportOutputDefaultWithScreen[3] FAILED [ 32%] test/integration/clitest/test_import.py::TestImport::testImportAsRoot PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testImportMultiGroup PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testImportAsRootMultiGroup PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Image] PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Image-x] PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Image--description] PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Image-n] PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Image-n-x] PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Image-n--description] PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Image--name] PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Image--name-x] PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Image--name--description] PASSED [ 32%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate] FAILED [ 32%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate-x] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--description] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--plate_description] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate-n] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate-n-x] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate-n--description] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate-n--plate_description] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--name] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--name-x] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--name--description] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--name--plate_description] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--plate_name] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--plate_name-x] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--plate_name--description] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--plate_name--plate_description] FAILED [ 33%] test/integration/clitest/test_import.py::TestImport::testNoThumbnails[--no-thumbnails] PASSED [ 33%] test/integration/clitest/test_import.py::TestImport::testNoThumbnails[--no_thumbnails] PASSED [ 33%] test/integration/clitest/test_import.py::TestImport::testSkipArguments[] PASSED [ 33%] test/integration/clitest/test_import.py::TestImport::testSkipArguments[all] PASSED [ 33%] test/integration/clitest/test_import.py::TestImport::testSkipArguments[checksum] PASSED [ 33%] test/integration/clitest/test_import.py::TestImport::testSkipArguments[minmax] PASSED [ 34%] test/integration/clitest/test_import.py::TestImport::testSkipArguments[thumbnails] PASSED [ 34%] test/integration/clitest/test_import.py::TestImport::testSkipArguments[upgrade] PASSED [ 34%] test/integration/clitest/test_import.py::TestImport::testSymlinkImport PASSED [ 34%] test/integration/clitest/test_import.py::TestImport::testUnknownTarget[Dataset-test.fake--d] PASSED [ 34%] test/integration/clitest/test_import.py::TestImport::testUnknownTarget[Screen-SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake--r] PASSED [ 34%] test/integration/clitest/test_import.py::TestImport::testEncryption[] PASSED [ 34%] test/integration/clitest/test_import.py::TestImport::testEncryption[--encrypted=false] PASSED [ 34%] test/integration/clitest/test_import.py::TestImport::testEncryption[--encrypted=true] PASSED [ 34%] test/integration/clitest/test_import.py::TestImport::testBulk PASSED [ 34%] test/integration/clitest/test_import.py::TestImport::testParallelUpload PASSED [ 34%] test/integration/clitest/test_import.py::TestImport::testParallelFileset PASSED [ 34%] test/integration/clitest/test_import.py::TestImport::testBulkImportLogs PASSED [ 34%] test/integration/clitest/test_import_bulk.py::TestImportBulk::testBulk PASSED [ 34%] test/integration/clitest/test_ldap.py::TestLDAP::testAdminOnly[active] PASSED [ 34%] test/integration/clitest/test_ldap.py::TestLDAP::testAdminOnly[discover] PASSED [ 34%] test/integration/clitest/test_ldap.py::TestLDAP::testAdminOnly[create] PASSED [ 34%] test/integration/clitest/test_ldap.py::TestLDAP::testAdminOnly[getdn] PASSED [ 34%] test/integration/clitest/test_ldap.py::TestLDAP::testAdminOnly[setdn] PASSED [ 34%] test/integration/clitest/test_metadata.py::TestMetadata::test_get_identifiers PASSED [ 34%] test/integration/clitest/test_metadata.py::TestMetadata::test_get_parents[False] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadata::test_get_parents[True] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadata::test_get_roi_count[0] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadata::test_get_roi_count[1] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadata::test_get_original PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadata::test_get_bulkanns[False] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadata::test_get_bulkanns[True] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadata::test_get_measures[False] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadata::test_get_measures[True] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadata::test_get_allanns[False] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadata::test_get_allanns[True] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadataControl::test_original PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadataControl::test_bulkanns[False] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadataControl::test_bulkanns[True] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadataControl::test_measures[False] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadataControl::test_measures[True] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadataControl::test_mapanns[False] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadataControl::test_mapanns[True] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadataControl::test_allanns[False] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadataControl::test_allanns[True] PASSED [ 35%] test/integration/clitest/test_metadata.py::TestMetadataControl::test_pixelsize PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_create_from_file PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_create_from_args PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_linkage PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_linkage_via_variables PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_required[input0] PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_required[input1] PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_required[input2] PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_link_annotation PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_new_get_and_update PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_fail_leading_numbers_argument PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_argument_with_letters_and_numbers PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_new_and_get_obj PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_get_unit_and_value PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_get_unknown_and_empty_field PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_get_fields PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_get_list_field PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_list_get PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_map_mods PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_nulling PASSED [ 36%] test/integration/clitest/test_obj.py::TestObj::test_newlines PASSED [ 37%] test/integration/clitest/test_pyramids.py::TestRemovePyramids::test_removepyramids_admin_only PASSED [ 37%] test/integration/clitest/test_pyramids.py::TestRemovePyramidsRestrictedAdmin::test_removepyramids_restricted_admin PASSED [ 37%] test/integration/clitest/test_pyramids.py::TestRemovePyramidsFullAdmin::test_remove_pyramids_little_endian PASSED [ 37%] test/integration/clitest/test_pyramids.py::TestRemovePyramidsFullAdmin::test_remove_pyramids_imported_after_future PASSED [ 37%] test/integration/clitest/test_pyramids.py::TestRemovePyramidsFullAdmin::test_remove_pyramids_limit PASSED [ 37%] test/integration/clitest/test_pyramids.py::TestRemovePyramidsFullAdmin::test_remove_pyramids_not_valid_limit PASSED [ 37%] test/integration/clitest/test_pyramids.py::TestRemovePyramidsFullAdmin::test_remove_pyramids_manual SKIPPED [ 37%] test/integration/clitest/test_pyramids.py::TestRemovePyramidsFullAdmin::test_remove__pre_fs_pyramids PASSED [ 37%] test/integration/clitest/test_pyramids.py::TestRemovePyramidsFullAdmin::test_remove_pyramids_big_endian PASSED [ 37%] test/integration/clitest/test_pyramids.py::TestRemovePyramidsFullAdmin::test_remove_pyramids PASSED [ 37%] test/integration/clitest/test_pyramids.py::TestRemovePyramidsFullAdmin::test_remove_pyramids_check_thumbnails PASSED [ 37%] test/integration/clitest/test_script.py::TestScript::testList PASSED [ 37%] test/integration/clitest/test_script.py::TestScript::testDemo PASSED [ 37%] test/integration/clitest/test_script.py::TestScript::testFullSession PASSED [ 37%] test/integration/clitest/test_script.py::TestScript::testReplace PASSED [ 37%] test/integration/clitest/test_script.py::TestScript::testReplaceOfficial PASSED [ 37%] test/integration/clitest/test_search.py::TestSearch::test_search_basic PASSED [ 37%] test/integration/clitest/test_search.py::TestSearch::test_search_wildcard PASSED [ 37%] test/integration/clitest/test_search.py::TestSearch::test_search_name_field PASSED [ 37%] test/integration/clitest/test_search.py::TestSearch::test_search_description_field PASSED [ 37%] test/integration/clitest/test_search.py::TestSearch::test_search_style PASSED [ 38%] test/integration/clitest/test_search.py::TestSearch::test_search_ids_only PASSED [ 38%] test/integration/clitest/test_search.py::TestSearch::test_search_acquisition_date[data0] PASSED [ 38%] test/integration/clitest/test_search.py::TestSearch::test_search_acquisition_date[data1] PASSED [ 38%] test/integration/clitest/test_search.py::TestSearch::test_search_other_dates[data0] PASSED [ 38%] test/integration/clitest/test_search.py::TestSearch::test_search_other_dates[data1] PASSED [ 38%] test/integration/clitest/test_search.py::TestSearch::test_search_other_dates[data2] PASSED [ 38%] test/integration/clitest/test_search.py::TestSearch::test_search_other_dates[data3] PASSED [ 38%] test/integration/clitest/test_search.py::TestSearch::test_search_other_dates[data4] PASSED [ 38%] test/integration/clitest/test_search.py::TestSearch::test_search_no_parse PASSED [ 38%] test/integration/clitest/test_search.py::TestSearch::test_search_dataset_acquisition PASSED [ 38%] test/integration/clitest/test_search.py::TestSearch::test_search_index_by_user PASSED [ 38%] test/integration/clitest/test_sessions.py::TestSessions::testLogin[None-True] PASSED [ 38%] test/integration/clitest/test_sessions.py::TestSessions::testLogin[None-False] PASSED [ 38%] test/integration/clitest/test_sessions.py::TestSessions::testLogin[300-True] PASSED [ 38%] test/integration/clitest/test_sessions.py::TestSessions::testLogin[300-False] PASSED [ 38%] test/integration/clitest/test_sessions.py::TestSessions::testLoginAs[rw----] PASSED [ 38%] test/integration/clitest/test_sessions.py::TestSessions::testLoginAs[rwr---] PASSED [ 38%] test/integration/clitest/test_sessions.py::TestSessions::testLoginAs[rwra--] PASSED [ 38%] test/integration/clitest/test_sessions.py::TestSessions::testLoginAs[rwrw--] PASSED [ 38%] test/integration/clitest/test_sessions.py::TestSessions::testLoginMultiGroup[True-True] PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::testLoginMultiGroup[True-False] PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::testLoginMultiGroup[False-True] PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::testLoginMultiGroup[False-False] PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::testGroup PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::testTimeout PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::testFile PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::testKey PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::testWho[user] PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::testWho[root] PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::test_open PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::test_open_with_id PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::test_open_restricted_admin_no_sudo PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::test_open_restricted_admin_sudo PASSED [ 39%] test/integration/clitest/test_sessions.py::TestSessions::test_close PASSED [ 39%] test/integration/clitest/test_tag.py::TestTag::testCreateTag[None-None] PASSED [ 39%] test/integration/clitest/test_tag.py::TestTag::testCreateTag[None---name] PASSED [ 39%] test/integration/clitest/test_tag.py::TestTag::testCreateTag[--description-None] PASSED [ 39%] test/integration/clitest/test_tag.py::TestTag::testCreateTag[--description---name] PASSED [ 39%] test/integration/clitest/test_tag.py::TestTag::testCreateTagset[None-None] PASSED [ 39%] test/integration/clitest/test_tag.py::TestTag::testCreateTagset[None---name] PASSED [ 40%] test/integration/clitest/test_tag.py::TestTag::testCreateTagset[--desc-None] PASSED [ 40%] test/integration/clitest/test_tag.py::TestTag::testCreateTagset[--desc---name] PASSED [ 40%] test/integration/clitest/test_tag.py::TestTag::testLoadTag PASSED [ 40%] test/integration/clitest/test_tag.py::TestTag::testLoadTagset PASSED [ 40%] test/integration/clitest/test_tag.py::TestTag::testLink[Image] PASSED [ 40%] test/integration/clitest/test_tag.py::TestTag::testLink[Dataset] PASSED [ 40%] test/integration/clitest/test_tag.py::TestTag::testLink[Project] PASSED [ 40%] test/integration/clitest/test_tag.py::TestTag::testLink[Screen] PASSED [ 40%] test/integration/clitest/test_tag.py::TestTag::testLink[Plate] PASSED [ 40%] test/integration/clitest/test_tag.py::TestTag::testLinkInvalidObject PASSED [ 40%] test/integration/clitest/test_tag.py::TestTag::testLinkInvalidTag PASSED [ 40%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rw-----admin-admin] PASSED [ 40%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rw-----admin-owner] PASSED [ 40%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rw-----admin-member] PASSED [ 40%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rw-----owner-admin] PASSED [ 40%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rw-----owner-owner] PASSED [ 40%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rw-----owner-member] PASSED [ 40%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rw-----member-admin] PASSED [ 40%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rw-----member-owner] PASSED [ 40%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rw-----member-member] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwr----admin-admin] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwr----admin-owner] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwr----admin-member] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwr----owner-admin] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwr----owner-owner] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwr----owner-member] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwr----member-admin] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwr----member-owner] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwr----member-member] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwra---admin-admin] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwra---admin-owner] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwra---admin-member] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwra---owner-admin] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwra---owner-owner] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwra---owner-member] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwra---member-admin] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwra---member-owner] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwra---member-member] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwrw---admin-admin] PASSED [ 41%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwrw---admin-owner] PASSED [ 42%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwrw---admin-member] PASSED [ 42%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwrw---owner-admin] PASSED [ 42%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwrw---owner-owner] PASSED [ 42%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwrw---owner-member] PASSED [ 42%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwrw---member-admin] PASSED [ 42%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwrw---member-owner] PASSED [ 42%] test/integration/clitest/test_tag.py::TestPermissions::testLink[rwrw---member-member] PASSED [ 42%] test/integration/clitest/test_tag.py::TestTagList::testList[] PASSED [ 42%] test/integration/clitest/test_tag.py::TestTagList::testList[--nopage] PASSED [ 42%] test/integration/clitest/test_tag.py::TestTagList::testListSets[] PASSED [ 42%] test/integration/clitest/test_tag.py::TestTagList::testListSets[--nopage] PASSED [ 42%] test/integration/clitest/test_upload.py::TestUpload::testUploadSingleFile PASSED [ 42%] test/integration/clitest/test_upload.py::TestUpload::testUploadMultipleFiles PASSED [ 42%] test/integration/clitest/test_upload.py::TestUpload::testUploadBadFile PASSED [ 42%] test/integration/clitest/test_user.py::TestUser::testList[None-None] PASSED [ 42%] test/integration/clitest/test_user.py::TestUser::testList[None-id] PASSED [ 42%] test/integration/clitest/test_user.py::TestUser::testList[None-login] PASSED [ 42%] test/integration/clitest/test_user.py::TestUser::testList[None-first-name] PASSED [ 42%] test/integration/clitest/test_user.py::TestUser::testList[None-last-name] PASSED [ 42%] test/integration/clitest/test_user.py::TestUser::testList[None-email] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testList[count-None] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testList[count-id] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testList[count-login] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testList[count-first-name] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testList[count-last-name] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testList[count-email] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testList[long-None] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testList[long-id] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testList[long-login] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testList[long-first-name] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testList[long-last-name] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testList[long-email] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testListWithStyles[None] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testListWithStyles[sql] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testListWithStyles[csv] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testListWithStyles[plain] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testListWithStyles[json] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testInfoNoArgument PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testInfoArgument[id] PASSED [ 43%] test/integration/clitest/test_user.py::TestUser::testInfoArgument[omeName] PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testInfoArgument[--user-id] PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testInfoArgument[--user-name] PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testInfoInvalidUser PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testListGroupsNoArgument PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testListGroupsArgument[id] PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testListGroupsArgument[omeName] PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testListGroupsArgument[--user-id] PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testListGroupsArgument[--user-name] PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testListGroupsInvalidArgument PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testEmail[None] PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testEmail[-1] PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testEmail[--one] PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testPassword[True] PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testPassword[False] PASSED [ 44%] test/integration/clitest/test_user.py::TestUser::testAddAdminOnly PASSED [ 44%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[None-id---id] PASSED [ 44%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[None-id---name] PASSED [ 44%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[None-name---id] PASSED [ 44%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[None-name---name] PASSED [ 44%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[None---group-id---id] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[None---group-id---name] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[None---group-name---id] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[None---group-name---name] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[--as-owner-id---id] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[--as-owner-id---name] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[--as-owner-name---id] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[--as-owner-name---name] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[--as-owner---group-id---id] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[--as-owner---group-id---name] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[--as-owner---group-name---id] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testJoinGroup[--as-owner---group-name---name] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-True-id---id] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-True-id---name] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-True-name---id] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-True-name---name] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-True---group-id---id] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-True---group-id---name] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-True---group-name---id] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-True---group-name---name] PASSED [ 45%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-False-id---id] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-False-id---name] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-False-name---id] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-False-name---name] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-False---group-id---id] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-False---group-id---name] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-False---group-name---id] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[None-False---group-name---name] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-True-id---id] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-True-id---name] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-True-name---id] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-True-name---name] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-True---group-id---id] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-True---group-id---name] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-True---group-name---id] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-True---group-name---name] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-False-id---id] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-False-id---name] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-False-name---id] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-False-name---name] PASSED [ 46%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-False---group-id---id] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-False---group-id---name] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-False---group-name---id] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testLeaveGroup[--as-owner-False---group-name---name] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None-None-None-None] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None-None-None--m] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None-None-None---middlename] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None-None--e-None] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None-None--e--m] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None-None--e---middlename] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None-None---email-None] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None-None---email--m] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None-None---email---middlename] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None--i-None-None] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None--i-None--m] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None--i-None---middlename] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None--i--e-None] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None--i--e--m] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None--i--e---middlename] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None--i---email-None] PASSED [ 47%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None--i---email--m] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None--i---email---middlename] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None---institution-None-None] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None---institution-None--m] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None---institution-None---middlename] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None---institution--e-None] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None---institution--e--m] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None---institution--e---middlename] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None---institution---email-None] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None---institution---email--m] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[None---institution---email---middlename] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a-None-None-None] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a-None-None--m] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a-None-None---middlename] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a-None--e-None] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a-None--e--m] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a-None--e---middlename] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a-None---email-None] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a-None---email--m] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a-None---email---middlename] PASSED [ 48%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a--i-None-None] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a--i-None--m] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a--i-None---middlename] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a--i--e-None] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a--i--e--m] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a--i--e---middlename] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a--i---email-None] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a--i---email--m] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a--i---email---middlename] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a---institution-None-None] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a---institution-None--m] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a---institution-None---middlename] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a---institution--e-None] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a---institution--e--m] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a---institution--e---middlename] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a---institution---email-None] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a---institution---email--m] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[-a---institution---email---middlename] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin-None-None-None] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin-None-None--m] PASSED [ 49%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin-None-None---middlename] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin-None--e-None] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin-None--e--m] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin-None--e---middlename] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin-None---email-None] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin-None---email--m] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin-None---email---middlename] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin--i-None-None] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin--i-None--m] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin--i-None---middlename] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin--i--e-None] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin--i--e--m] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin--i--e---middlename] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin--i---email-None] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin--i---email--m] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin--i---email---middlename] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin---institution-None-None] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin---institution-None--m] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin---institution-None---middlename] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin---institution--e-None] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin---institution--e--m] PASSED [ 50%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin---institution--e---middlename] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin---institution---email-None] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin---institution---email--m] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAdd[--admin---institution---email---middlename] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAddGroup[id] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAddGroup[name] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAddGroup[--group-id] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAddGroup[--group-name] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAddPassword[True-None] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAddPassword[True--P] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAddPassword[True---userpassword] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAddPassword[False-None] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAddPassword[False--P] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAddPassword[False---userpassword] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testAddNoPassword PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testPassword[True] PASSED [ 51%] test/integration/clitest/test_user.py::TestUserRoot::testPassword[False] PASSED [ 51%] test/integration/fstest/test_rename.py::TestRename::test_rename_permissions[data0] PASSED [ 51%] test/integration/fstest/test_rename.py::TestRename::test_rename_permissions[data1] PASSED [ 51%] test/integration/fstest/test_rename.py::TestRename::test_rename_permissions[data2] PASSED [ 51%] test/integration/fstest/test_rename.py::TestRename::test_rename_permissions[data3] PASSED [ 52%] test/integration/fstest/test_rename.py::TestRename::test_rename_permissions[data4] PASSED [ 52%] test/integration/fstest/test_rename.py::TestRename::test_rename_annotation PASSED [ 52%] test/integration/fstest/test_rename.py::TestRename::test_prep_and_delete PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testSameOwner PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testCommentAnnotation PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testNonDefGroupAnnotation PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testTimestampAnnotation PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testBooleanAnnotation PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testLongAnnotation PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testMapAnnotation PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testDualLinkedAnnotation PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testListAnnotations PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testFileAnnotation PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testFileAnnotationNoName PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testFileAnnotationSpeed PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testFileAnnNonDefaultGroup PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testUnlinkAnnotation PASSED [ 52%] test/integration/gatewaytest/test_annotation.py::testAnnotationCount PASSED [ 52%] test/integration/gatewaytest/test_chgrp.py::testImageChgrp PASSED [ 52%] test/integration/gatewaytest/test_chgrp.py::testDatasetChgrp PASSED [ 53%] test/integration/gatewaytest/test_chgrp.py::testPDIChgrp PASSED [ 53%] test/integration/gatewaytest/test_chgrp.py::testTwoDatasetsChgrpToProject PASSED [ 53%] test/integration/gatewaytest/test_chgrp.py::testMultiDatasetDoAll PASSED [ 53%] test/integration/gatewaytest/test_chmod.py::TestChmodGroup::testChmod PASSED [ 53%] test/integration/gatewaytest/test_chmod.py::TestCustomUsers::testReadOnly PASSED [ 53%] test/integration/gatewaytest/test_chmod.py::TestCustomUsers::testReadAnnotate PASSED [ 53%] test/integration/gatewaytest/test_chmod.py::TestCustomUsers::testGroupMinusOne PASSED [ 53%] test/integration/gatewaytest/test_chmod.py::TestCustomUsers::testReadWrite PASSED [ 53%] test/integration/gatewaytest/test_chmod.py::TestCustomUsers::testDelete8723 PASSED [ 53%] test/integration/gatewaytest/test_chmod.py::TestManualCreateEdit::testReadOnly PASSED [ 53%] test/integration/gatewaytest/test_chmod.py::Test8800::testWithBlitzWrappers PASSED [ 53%] test/integration/gatewaytest/test_chmod.py::Test8800::testWithoutWrappers PASSED [ 53%] test/integration/gatewaytest/test_chmod.py::TestDefaultSetup::testAuthorCanEdit PASSED [ 53%] test/integration/gatewaytest/test_chown.py::TestChown::test_chown_project PASSED [ 53%] test/integration/gatewaytest/test_chown.py::TestChown::test_chown_pdi PASSED [ 53%] test/integration/gatewaytest/test_config_service.py::testInterpolateSetting[foo] PASSED [ 53%] test/integration/gatewaytest/test_config_service.py::testInterpolateSetting[False] PASSED [ 53%] test/integration/gatewaytest/test_config_service.py::testInterpolateSetting[false] PASSED [ 53%] test/integration/gatewaytest/test_config_service.py::testInterpolateSetting[True] PASSED [ 53%] test/integration/gatewaytest/test_config_service.py::testInterpolateSetting[true] PASSED [ 54%] test/integration/gatewaytest/test_config_service.py::testInterpolateSetting[] PASSED [ 54%] test/integration/gatewaytest/test_config_service.py::testInterpolateSetting[None] PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testMultiProcessSession PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testClose ERROR [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testTopLevelObjects ERROR [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testCloseSession PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testMiscellaneous PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testConnectUsingClient PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testConnectUsingClientNoSessionWithIdentity PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testConnectUsingClientSessionWithoutIdentity PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testSessionId PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testConnectWithSessionId PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testSecureWithSecureClient PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testSecureWithUnsecureClient PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testSecureWithUsername[None] PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testSecureWithUsername[False] PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testSecureWithUsername[True] PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testSecureMisMatch PASSED [ 54%] test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testHost PASSED [ 54%] test/integration/gatewaytest/test_delete.py::TestDelete::testDeleteObjectsUnwrapped PASSED [ 55%] test/integration/gatewaytest/test_delete.py::TestDelete::testDeleteObjects PASSED [ 55%] test/integration/gatewaytest/test_delete.py::TestDelete::testDeleteObjectsWait PASSED [ 55%] test/integration/gatewaytest/test_delete.py::TestDelete::testDeleteObjectsDryRun PASSED [ 55%] test/integration/gatewaytest/test_delete.py::TestDelete::testDeleteAnnotatedFileAnnotation PASSED [ 55%] test/integration/gatewaytest/test_delete.py::TestDelete::testDeleteObjectDirect PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testCountArchivedFiles PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testCountFilesetFiles PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testCountImportedImageFiles PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testGetImportedFilesInfo PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testGetImportedFilesInfoWithAnnotations PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testGetArchivedFiles PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testGetImportedImageFiles PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testGetArchivedFilesInfo PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testGetFilesetFilesInfo PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testGetFilesetFilesInfoWithAnnotations PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testGetFilesetFilesInfoMultiple PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testGetFilesetFilesInfoMultipleWithAnnotations PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testGetFileset PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestFileset::testGetImportedImageFilePaths PASSED [ 55%] test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testCountArchivedFiles PASSED [ 56%] test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testCountFilesetFiles PASSED [ 56%] test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testCountImportedImageFiles PASSED [ 56%] test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testGetImportedFilesInfo PASSED [ 56%] test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testGetArchivedFiles PASSED [ 56%] test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testGetImportedImageFiles PASSED [ 56%] test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testGetArchivedFilesInfo PASSED [ 56%] test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testGetFilesetFilesInfo PASSED [ 56%] test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testGetFilesetFilesInfoMultiple PASSED [ 56%] test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testGetFileset PASSED [ 56%] test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testGetImportedImageFilePaths PASSED [ 56%] test/integration/gatewaytest/test_get_objects.py::TestDeleteObject::testDeleteAnnotation PASSED [ 56%] test/integration/gatewaytest/test_get_objects.py::TestDeleteObject::testDeleteImage PASSED [ 56%] test/integration/gatewaytest/test_get_objects.py::TestFindObject::testIllegalObjTypeInt PASSED [ 56%] test/integration/gatewaytest/test_get_objects.py::TestFindObject::testObjTypeUnicode PASSED [ 56%] test/integration/gatewaytest/test_get_objects.py::TestFindObject::testObjTypeString PASSED [ 56%] test/integration/gatewaytest/test_get_objects.py::TestFindObject::testFindProject PASSED [ 56%] test/integration/gatewaytest/test_get_objects.py::TestFindObject::testFindExperimenter PASSED [ 56%] test/integration/gatewaytest/test_get_objects.py::TestFindObject::testFindAnnotation PASSED [ 56%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testSearchObjects PASSED [ 56%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testListProjects PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testPagination PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetDatasetsByProject PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testListExperimentersAndGroups[True] PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testListExperimentersAndGroups[False] PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testListColleagues PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testFindExperimenterWithGroups PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetExperimentersByGroup[True] PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetExperimentersByGroup[False] PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetExperimenter PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetAnnotations PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetImage PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetImageLoadPixels[True-True] PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetImageLoadPixels[True-False] PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetImageLoadPixels[False-True] PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetImageLoadPixels[False-False] PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetProject PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testTraversal PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testListOrphans[False0-True] PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testListOrphans[False0-False] PASSED [ 57%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testListOrphans[False1-True] PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testListOrphans[False1-False] PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testOrderById PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetObjectsByMapAnnotations[Image] PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetObjectsByMapAnnotations[Dataset] PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetObjectsByMapAnnotations[Project] PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetObjectsByMapAnnotations[Screen] PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestGetObject::testGetObjectsByMapAnnotations[Plate] PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestLeaderAndMemberOfGroup::testGetGroupsLeaderOfAsLeader PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestLeaderAndMemberOfGroup::testGetGroupsLeaderOfAsMember PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestLeaderAndMemberOfGroup::testGetGroupsMemberOf PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestLeaderAndMemberOfGroup::testGroupSummaryAsOwner PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestLeaderAndMemberOfGroup::testGroupSummaryAsMember PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestLeaderAndMemberOfGroup::testGroupSummaryAsOwnerDeprecated PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestLeaderAndMemberOfGroup::testGroupSummaryAsMemberDeprecated PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestListParents::testSupportedObjects PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestListParents::testListParentsPDI PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestListParents::testListParentsSPW PASSED [ 58%] test/integration/gatewaytest/test_get_objects.py::TestListParents::testExperimenterListParents PASSED [ 58%] test/integration/gatewaytest/test_helpers.py::TestHelperObjects::testColorHolder PASSED [ 58%] test/integration/gatewaytest/test_helpers.py::TestHelperObjects::testOmeroType PASSED [ 59%] test/integration/gatewaytest/test_helpers.py::TestHelperObjects::testSplitHTMLColor PASSED [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testThumbnail ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testThumbnailSet ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testRenderingModels ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testSplitChannel ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testLinePlots ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testProjections ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testProperties ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testPixelSizeUnits ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testUnitsGetValue ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testChannelWavelengthUnits ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testExposureTimeUnits ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testShortname ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testImageDate ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testSimpleMarshal ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testExport ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testRenderJpegRegion ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testRenderJpegRegion_resolution ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testRenderJpegRegion_invalid_resolution ERROR [ 59%] test/integration/gatewaytest/test_image.py::TestImage::testRenderBirdsEyeView ERROR [ 60%] test/integration/gatewaytest/test_image.py::TestImage::testRenderBirdsEyeView_Size ERROR [ 60%] test/integration/gatewaytest/test_image_wrapper.py::TestImageWrapper::testGetDate PASSED [ 60%] test/integration/gatewaytest/test_image_wrapper.py::TestImageWrapper::testGetDateNoAcquisitionDate PASSED [ 60%] test/integration/gatewaytest/test_image_wrapper.py::TestImageWrapper::testSimpleMarshal PASSED [ 60%] test/integration/gatewaytest/test_image_wrapper.py::TestImageWrapper::testChannelLabel PASSED [ 60%] test/integration/gatewaytest/test_image_wrapper.py::TestImageWrapper::testChannelEmissionWaveLabel PASSED [ 60%] test/integration/gatewaytest/test_image_wrapper.py::TestImageWrapper::testChannelNoLabel PASSED [ 60%] test/integration/gatewaytest/test_missing_pyramid.py::TestPyramid::testThrowException PASSED [ 60%] test/integration/gatewaytest/test_missing_pyramid.py::TestPyramid::testPrepareRenderingEngine PASSED [ 60%] test/integration/gatewaytest/test_missing_pyramid.py::TestPyramid::testGetChannels PASSED [ 60%] test/integration/gatewaytest/test_missing_pyramid.py::TestPyramid::testGetChannelsNoRe PASSED [ 60%] test/integration/gatewaytest/test_missing_pyramid.py::TestPyramid::testGetRdefId PASSED [ 60%] test/integration/gatewaytest/test_permissions.py::TestPrivileges::test_update_admin_privileges PASSED [ 60%] test/integration/gatewaytest/test_permissions.py::TestPrivileges::test_full_admin_privileges PASSED [ 60%] test/integration/gatewaytest/test_pixels.py::TestPixels::testReuseRawPixelsStore ERROR [ 60%] test/integration/gatewaytest/test_pixels.py::TestPixels::testPlaneInfo ERROR [ 60%] test/integration/gatewaytest/test_pixels.py::TestPixels::testPixelsType ERROR [ 60%] test/integration/gatewaytest/test_pixels.py::TestPixels::testGetTile ERROR [ 60%] test/integration/gatewaytest/test_pixels.py::TestPixels::testGetPlane ERROR [ 60%] test/integration/gatewaytest/test_pixels.py::TestPixels::testGetPlanesExceptionOnGetPlane ERROR [ 61%] test/integration/gatewaytest/test_pixels.py::TestPixels::testGetPlanesExceptionOnClose ERROR [ 61%] test/integration/gatewaytest/test_pixels.py::TestPixels::testGetPlanesExceptionOnBoth ERROR [ 61%] test/integration/gatewaytest/test_pixels.py::TestPixels::testGetHistogram ERROR [ 61%] test/integration/gatewaytest/test_plate_wrapper.py::TestPlateWrapper::testGetGridSize PASSED [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testDefault ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testCustomized ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testChannelWindows ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testFloatDefaultMinMax ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testEmissionWave ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testBatchCopy ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testGroupBasedPermissions ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testGetRdefs ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testResetDefaults ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testQuantizationSettings ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testQuantizationSettingsInvalid ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testQuantizationSettingsBulk ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testGetChannelsNoRE ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testSetActiveChannelsNoRE ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testSetActiveChannelsWithRE ERROR [ 61%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::test_set_active_channels_set_inactive[True] ERROR [ 62%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::test_set_active_channels_set_inactive[False] ERROR [ 62%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testUnregisterService ERROR [ 62%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testRegisterService ERROR [ 62%] test/integration/gatewaytest/test_rdefs.py::TestRDefs::testCloseRE ERROR [ 62%] test/integration/gatewaytest/test_search_objects.py::TestGetObject::testSearchObjects PASSED [ 62%] test/integration/gatewaytest/test_services.py::TestServices::testDeleteServiceAuthor PASSED [ 62%] test/integration/gatewaytest/test_services.py::TestServices::testDeleteServiceAdmin PASSED [ 62%] test/integration/gatewaytest/test_services.py::TestTables::testTableRead PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rw_root_dirTrue_grpTrue_16 PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rw_root_dirTrue_grpTrue_96 PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rw_root_dirTrue_grpFalse_16 PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rw_root_dirTrue_grpFalse_96 PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rw_root_dirFalse_grpTrue_16 PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rw_root_dirFalse_grpTrue_96 PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rw_root_dirFalse_grpFalse_16 PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rw_root_dirFalse_grpFalse_96 PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_root_dirTrue_grpTrue_16 PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_root_dirTrue_grpTrue_96 PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_root_dirTrue_grpFalse_16 PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_root_dirTrue_grpFalse_96 PASSED [ 62%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_root_dirFalse_grpTrue_16 PASSED [ 63%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_root_dirFalse_grpTrue_96 PASSED [ 63%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_root_dirFalse_grpFalse_16 PASSED [ 63%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_root_dirFalse_grpFalse_96 PASSED [ 63%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_member_dirTrue_grpTrue_16 PASSED [ 63%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_member_dirTrue_grpTrue_96 PASSED [ 63%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_member_dirTrue_grpFalse_16 PASSED [ 63%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_member_dirTrue_grpFalse_96 PASSED [ 63%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_member_dirFalse_grpTrue_16 PASSED [ 63%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_member_dirFalse_grpTrue_96 PASSED [ 63%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_member_dirFalse_grpFalse_16 PASSED [ 63%] test/integration/gatewaytest/test_ticket10618.py::Test10618::test_rwr_member_dirFalse_grpFalse_96 PASSED [ 63%] test/integration/gatewaytest/test_user.py::TestUser::testUsers PASSED [ 63%] test/integration/gatewaytest/test_user.py::TestUser::testSaveAs FAILED [ 63%] test/integration/gatewaytest/test_user.py::TestUser::testCrossGroupSave PASSED [ 63%] test/integration/gatewaytest/test_user.py::TestUser::testGroupOverObjPermissions PASSED [ 63%] test/integration/gatewaytest/test_wrapper.py::TestWrapper::testAllObjectsWrapped ERROR [ 63%] test/integration/gatewaytest/test_wrapper.py::TestWrapper::testProjectWrapper PASSED [ 63%] test/integration/gatewaytest/test_wrapper.py::TestWrapper::testDatasetWrapper ERROR [ 63%] test/integration/gatewaytest/test_wrapper.py::TestWrapper::testExperimenterWrapper PASSED [ 63%] test/integration/gatewaytest/test_wrapper.py::TestWrapper::testDetailsWrapper ERROR [ 64%] test/integration/gatewaytest/test_wrapper.py::TestWrapper::testOriginalFileWrapperGetFileInChunks PASSED [ 64%] test/integration/gatewaytest/test_wrapper.py::TestWrapper::testOriginalFileWrapperAsFileObj PASSED [ 64%] test/integration/gatewaytest/test_wrapper.py::TestWrapper::testOriginalFileWrapperAsFileObjContextManager PASSED [ 64%] test/integration/gatewaytest/test_wrapper.py::TestWrapper::testOriginalFileWrapperAsFileObjMultiple PASSED [ 64%] test/integration/gatewaytest/test_wrapper.py::TestWrapper::testSetters PASSED [ 64%] test/integration/gatewaytest/test_wrapper.py::TestWrapper::testOther PASSED [ 64%] test/integration/metadata/test_metadata_mapannotations.py::TestMapAnnotationManager::test_add_from_namespace_query PASSED [ 64%] test/integration/metadata/test_metadata_mapannotations.py::TestMapAnnotationManager::test_add_from_namespace_query_duplicate PASSED [ 64%] test/integration/metadata/test_metadata_mapannotations.py::TestMapAnnotationManager::test_update_existing_mapann PASSED [ 64%] test/integration/metadata/test_populate.py::TestPopulateMetadataConfigLoad::test_get_config_local PASSED [ 64%] test/integration/metadata/test_populate.py::TestPopulateMetadataConfigLoad::test_get_config_remote PASSED [ 64%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[None-Screen2Plates] FAILED [ 64%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[None-Plate2Wells] FAILED [ 64%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[None-Dataset2Images] PASSED [ 64%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[None-Dataset2Images1Missing] PASSED [ 64%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[None-Dataset101Images] PASSED [ 64%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[None-Project2Datasets] PASSED [ 64%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[None-GZIP] PASSED [ 64%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[1-Screen2Plates] FAILED [ 64%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[1-Plate2Wells] FAILED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[1-Dataset2Images] PASSED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[1-Dataset2Images1Missing] PASSED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[1-Dataset101Images] PASSED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[1-Project2Datasets] PASSED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[1-GZIP] PASSED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[10-Screen2Plates] FAILED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[10-Plate2Wells] FAILED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[10-Dataset2Images] PASSED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[10-Dataset2Images1Missing] PASSED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[10-Dataset101Images] PASSED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[10-Project2Datasets] PASSED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[10-GZIP] PASSED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadataNsAnns[Plate2WellsNs] FAILED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadataNsAnns[Plate2WellsNs2] FAILED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadataNsAnnsUnavailableHeader FAILED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadataNsAnnsFail FAILED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadataDedup::testPopulateMetadataNsAnnsDedup[None] FAILED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadataDedup::testPopulateMetadataNsAnnsDedup[openmicroscopy.org/omero/bulk_annotations] FAILED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadataDedup::testPopulateMetadataNsAnnsDedup[openmicroscopy.org/mapr/gene] FAILED [ 65%] test/integration/metadata/test_populate.py::TestPopulateMetadataDedup::testPopulateMetadataNsAnnsDedupDelete[None] FAILED [ 66%] test/integration/metadata/test_populate.py::TestPopulateMetadataDedup::testPopulateMetadataNsAnnsDedupDelete[openmicroscopy.org/omero/bulk_annotations] FAILED [ 66%] test/integration/metadata/test_populate.py::TestPopulateMetadataDedup::testPopulateMetadataNsAnnsDedupDelete[openmicroscopy.org/mapr/gene] FAILED [ 66%] test/integration/metadata/test_populate.py::TestPopulateMetadataConfigFiles::test_delete_attach[True-None] FAILED [ 66%] test/integration/metadata/test_populate.py::TestPopulateMetadataConfigFiles::test_delete_attach[True-openmicroscopy.org/omero/bulk_annotations] FAILED [ 66%] test/integration/metadata/test_populate.py::TestPopulateMetadataConfigFiles::test_delete_attach[True-openmicroscopy.org/omero/bulk_annotations/config] FAILED [ 66%] test/integration/metadata/test_populate.py::TestPopulateMetadataConfigFiles::test_delete_attach[False-None] FAILED [ 66%] test/integration/metadata/test_populate.py::TestPopulateMetadataConfigFiles::test_delete_attach[False-openmicroscopy.org/omero/bulk_annotations] FAILED [ 66%] test/integration/metadata/test_populate.py::TestPopulateMetadataConfigFiles::test_delete_attach[False-openmicroscopy.org/omero/bulk_annotations/config] FAILED [ 66%] test/integration/metadata/test_populate.py::TestPopulateRois::testPopulateRoisPlate FAILED [ 66%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_get_format_filename_yaml[yaml] PASSED [ 66%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_get_format_filename_yaml[Yml] PASSED [ 66%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_get_format_filename_json[json] PASSED [ 66%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_get_format_filename_json[JS] PASSED [ 66%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_get_format_originalfileid_yaml[format0] PASSED [ 66%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_get_format_originalfileid_yaml[format1] PASSED [ 66%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_get_format_originalfileid_yaml[format2] PASSED [ 66%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_get_format_originalfileid_json[format0] PASSED [ 66%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_get_format_originalfileid_json[format1] PASSED [ 66%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_get_format_originalfileid_json[format2] PASSED [ 66%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_load[json-True] PASSED [ 67%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_load[json-False] PASSED [ 67%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_load[yaml-True] PASSED [ 67%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_load[yaml-False] PASSED [ 67%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_load_fromstring PASSED [ 67%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_load_invalidtype PASSED [ 67%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_dump[json] PASSED [ 67%] test/integration/metadata/test_pydict_text.py::TestPydictTextIo::test_dump[yaml] PASSED [ 67%] test/integration/scriptsharness/test_harness.py::TestScriptsViaOmeroCli::testDefinition PASSED [ 67%] test/integration/scriptsharness/test_harness.py::TestScriptsViaOmeroCli::testSimpleScript PASSED [ 67%] test/integration/scriptstest/test_cli.py::TestCLI::testCLI PASSED [ 67%] test/integration/scriptstest/test_coverage.py::TestCoverage::testGetScriptWithDetails PASSED [ 67%] test/integration/scriptstest/test_coverage.py::TestCoverage::testUploadAndScript PASSED [ 67%] test/integration/scriptstest/test_coverage.py::TestCoverage::testUserCantUploadOfficalScript PASSED [ 67%] test/integration/scriptstest/test_inputs.py::TestInputs::testInputs PASSED [ 67%] test/integration/scriptstest/test_ping.py::TestPing::testPingViaISCript PASSED [ 67%] test/integration/scriptstest/test_ping.py::TestPing::testPingParametersViaISCript PASSED [ 67%] test/integration/scriptstest/test_ping.py::TestPing::testPingStdout PASSED [ 67%] test/integration/scriptstest/test_ping.py::TestPing::testProcessShutdown PASSED [ 67%] test/integration/scriptstest/test_ping.py::TestPing::testProcessShutdownOneway PASSED [ 67%] test/integration/scriptstest/test_ping.py::TestPing::testProcessorGetResultsBeforeFinished PASSED [ 68%] test/integration/scriptstest/test_ping.py::TestPing::testProcessorExpires PASSED [ 68%] test/integration/scriptstest/test_ping.py::TestPing::testProcessorGetJob PASSED [ 68%] test/integration/scriptstest/test_ping.py::TestPing::testProcessorStop PASSED [ 68%] test/integration/scriptstest/test_ping.py::TestPing::testProcessorDetach PASSED [ 68%] test/integration/scriptstest/test_rand.py::TestRand::testRand PASSED [ 68%] test/integration/scriptstest/test_repo.py::TestScriptRepo::testScriptRepo PASSED [ 68%] test/integration/scriptstest/test_repo.py::TestScriptRepo::testGetOfficialScripts PASSED [ 68%] test/integration/scriptstest/test_repo.py::TestScriptRepo::testGetUserScripts PASSED [ 68%] test/integration/scriptstest/test_repo.py::TestScriptRepo::testCantUndulyLoadScriptRepoFromUuid PASSED [ 68%] test/integration/scriptstest/test_repo.py::TestScriptRepo::testMultipleScriptPathsNotSupported PASSED [ 68%] test/integration/scriptstest/test_repo.py::TestScriptRepo::testUploadingViaOfficialScriptShowsUpInRepo PASSED [ 68%] test/integration/scriptstest/test_repo.py::TestScriptRepo::testUploadingViaNonOfficialScriptDoesntShowUpInRepo PASSED [ 68%] test/integration/scriptstest/test_roi_handling_utils.py::TestRoiHandlingUtils::test_get_line_data PASSED [ 68%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_split_image PASSED [ 68%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_numpy_to_image PASSED [ 68%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_convert_numpy_array PASSED [ 68%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_numpy_save_as_image[True-tiff] PASSED [ 68%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_numpy_save_as_image[True-foo] PASSED [ 68%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_numpy_save_as_image[False-tiff] PASSED [ 68%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_numpy_save_as_image[False-foo] PASSED [ 69%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_create_file[] PASSED [ 69%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_create_file[text/x-python] PASSED [ 69%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_calc_sha1 PASSED [ 69%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_upload_file PASSED [ 69%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_download_file PASSED [ 69%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_get_objects PASSED [ 69%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_download_plane PASSED [ 69%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_upload_plane_by_row PASSED [ 69%] test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_upload_plane PASSED [ 69%] test/integration/tablestest/test_backwards_compatibility.py::TestBackwardsCompatibility_4_4_5::testCreateAllColumns_4_4_5 PASSED [ 69%] test/integration/tablestest/test_backwards_compatibility.py::TestBackwardsCompatibility_4_4_5::testAllColumns_4_4_5 PASSED [ 69%] test/integration/tablestest/test_backwards_compatibility.py::TestBackwardsCompatibility_4_4_5::testMetadataException PASSED [ 69%] test/integration/tablestest/test_backwards_compatibility.py::TestBackwardsCompatibility_5_3_4::testCreateAllColumnsAndMetadata_5_3_4 PASSED [ 69%] test/integration/tablestest/test_backwards_compatibility.py::TestBackwardsCompatibility_5_3_4::testAllColumnsAndMetadata_5_3_4 PASSED [ 69%] test/integration/tablestest/test_populate_metadata.py::TestPopulateMetadata::testPopulateMetadataPlate PASSED [ 69%] test/integration/tablestest/test_service.py::TestTables::testUpdate PASSED [ 69%] test/integration/tablestest/test_service.py::TestTables::testTicket2175 PASSED [ 69%] test/integration/tablestest/test_service.py::TestTables::testMask PASSED [ 69%] test/integration/tablestest/test_service.py::TestTables::test2855MetadataMethods PASSED [ 69%] test/integration/tablestest/test_service.py::TestTables::test2910 PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testDelete PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::test3714GetWhereListVars PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::test4000TableRead PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testCallContext PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testGetHeaders PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::test10049openTableUnreadable PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::test9971checkStringLength PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testArrayColumn PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testArrayColumnSize1 PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testAllColumnsSameTable PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::test10431uninitialisedTableReadWrite PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::test12606fileSizeCheck PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testCantWriteInternalMetadata[data0] PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testCantWriteInternalMetadata[data1] PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testCanWriteAlmostInternalMetadata[data0] PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testCanWriteAlmostInternalMetadata[data1] PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testCanReadInternalMetadata PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testColumnSpaceNames PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testIncludeRowNumbersSlice PASSED [ 70%] test/integration/tablestest/test_service.py::TestTables::testIncludeRowNumbersReadCoordinates PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testIncludeRowNumbersRead PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testSliceOrdering PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testReadCoordinatesOrdering PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testSliceEmptyInput PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testReadCoordinatesInvalidInput PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testReadInvalidInput PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testSliceInvalidInput PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testReadStartEnd PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testReadStartGreaterThanEnd PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testAddData PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testUpdateFirstRow PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testUpdateMultipleRows PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testUpdateAllows PASSED [ 71%] test/integration/tablestest/test_service.py::TestTables::testCannotUpdateOutOfRange PASSED [ 71%] test/integration/tablestest/test_tables.py::TestTableIntegrity::testAllColumnsAndMetadata PASSED [ 71%] test/integration/test_admin.py::TestAdmin::testGetGroup PASSED [ 71%] test/integration/test_admin.py::TestAdmin::testSetGroup PASSED [ 71%] test/integration/test_admin.py::TestAdmin::testChangePassword PASSED [ 71%] test/integration/test_admin.py::TestAdmin::testGetEventContext4011 PASSED [ 71%] test/integration/test_admin.py::TestAdmin::testUserRoles4056 PASSED [ 72%] test/integration/test_admin.py::TestAdmin::testSetSecurityPassword PASSED [ 72%] test/integration/test_annotation.py::TestFigureExportScripts::testAddAnnotations PASSED [ 72%] test/integration/test_annotationPermissions.py::TestPrivateGroup::testAddTag PASSED [ 72%] test/integration/test_annotationPermissions.py::TestPrivateGroup::testReadTag PASSED [ 72%] test/integration/test_annotationPermissions.py::TestPrivateGroup::testRemoveTag PASSED [ 72%] test/integration/test_annotationPermissions.py::TestReadOnlyGroup::testAddTag PASSED [ 72%] test/integration/test_annotationPermissions.py::TestReadOnlyGroup::testReadTag PASSED [ 72%] test/integration/test_annotationPermissions.py::TestReadOnlyGroup::testRemoveTag PASSED [ 72%] test/integration/test_annotationPermissions.py::TestReadAnnotateGroup::testAddTag PASSED [ 72%] test/integration/test_annotationPermissions.py::TestReadAnnotateGroup::testReadTag PASSED [ 72%] test/integration/test_annotationPermissions.py::TestReadAnnotateGroup::testRemoveTag PASSED [ 72%] test/integration/test_annotationPermissions.py::TestMovePrivatePermissions::testAddTagMakePrivate[root] PASSED [ 72%] test/integration/test_annotationPermissions.py::TestMovePrivatePermissions::testAddTagMakePrivate[admin] PASSED [ 72%] test/integration/test_annotationPermissions.py::TestMovePrivatePermissions::testAddTagMakePrivate[owner] PASSED [ 72%] test/integration/test_chgrp.py::TestChgrp::testChgrpImportedImage PASSED [ 72%] test/integration/test_chgrp.py::TestChgrp::testChgrpImage PASSED [ 72%] test/integration/test_chgrp.py::TestChgrp::testChgrpPDI PASSED [ 72%] test/integration/test_chgrp.py::TestChgrp::testChgrpRdef7825 PASSED [ 72%] test/integration/test_chgrp.py::TestChgrp::testChgrpOneImageFilesetErr PASSED [ 72%] test/integration/test_chgrp.py::TestChgrp::testChgrpAllImagesFilesetOK PASSED [ 73%] test/integration/test_chgrp.py::TestChgrp::testChgrpAllImagesFilesetTwoCommandsErr PASSED [ 73%] test/integration/test_chgrp.py::TestChgrp::testChgrpOneDatasetFilesetErr PASSED [ 73%] test/integration/test_chgrp.py::TestChgrp::testChgrpAllDatasetsFilesetOK PASSED [ 73%] test/integration/test_chgrp.py::TestChgrp::testChgrpOneDatasetFilesetOK PASSED [ 73%] test/integration/test_chgrp.py::TestChgrp::testChgrpImagesTwoFilesetsErr PASSED [ 73%] test/integration/test_chgrp.py::TestChgrp::testChgrpDatasetTwoFilesetsErr PASSED [ 73%] test/integration/test_chgrp.py::TestChgrp::testChgrpDatasetCheckFsGroup PASSED [ 73%] test/integration/test_chgrp.py::TestChgrp::testChgrpFilesetOK PASSED [ 73%] test/integration/test_chgrp.py::TestChgrp::testChgrp11000 PASSED [ 73%] test/integration/test_chgrp.py::TestChgrp::testChgrp11109 PASSED 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test/integration/test_isession.py::TestISession::testUpdateSessions[who1] PASSED [ 78%] test/integration/test_isession.py::TestISession::testUpdateSessions[who2] PASSED [ 78%] test/integration/test_isession.py::TestISession::testUpdateSessions[who3] PASSED [ 78%] test/integration/test_isession.py::TestISession::testUpdateSessionsNonAdminDisabling PASSED [ 78%] test/integration/test_isession.py::TestISession::testCreateSessionForGuest PASSED [ 78%] test/integration/test_isession.py::TestISession::test1018CreationDestructionClosing PASSED [ 79%] test/integration/test_isession.py::TestISession::testSimpleDestruction PASSED [ 79%] test/integration/test_isession.py::TestISession::testGetMySessionsTicket1975 PASSED [ 79%] test/integration/test_isession.py::TestISession::testTicket2196SetSecurityContext PASSED [ 79%] test/integration/test_isession.py::TestISession::testManageMySessions PASSED [ 79%] test/integration/test_isession.py::TestISession::testSessionWithIP[127.0.0.1] PASSED [ 79%] test/integration/test_isession.py::TestISession::testSessionWithIP[2400:cb00:2048:1::6814:55] PASSED [ 79%] test/integration/test_isession.py::TestISession::testSessionWithIP[1234:5678:1234:5678:1234:5678:121.212.121.212] PASSED [ 79%] test/integration/test_isession.py::TestISession::testCreateUserSession PASSED [ 79%] test/integration/test_isession.py::TestISession::testCreateUserSessionFromSudo[True] PASSED [ 79%] test/integration/test_isession.py::TestISession::testCreateUserSessionFromSudo[False] PASSED [ 79%] test/integration/test_ishare.py::TestIShare::test_that_permissions_are_default_private PASSED [ 79%] test/integration/test_ishare.py::TestIShare::test_basic_usage PASSED [ 79%] test/integration/test_ishare.py::TestIShare::test_canDoAction[canEdit] PASSED [ 79%] test/integration/test_ishare.py::TestIShare::test_canDoAction[canAnnotate] PASSED [ 79%] test/integration/test_ishare.py::TestIShare::test_canDoAction[canDelete] PASSED [ 79%] test/integration/test_ishare.py::TestIShare::test_canDoAction[canLink] PASSED [ 79%] test/integration/test_ishare.py::TestIShare::test8118 PASSED [ 79%] test/integration/test_ishare.py::TestIShare::test1154 PASSED [ 79%] test/integration/test_ishare.py::TestIShare::testCanAnnotate PASSED [ 79%] test/integration/test_ishare.py::TestIShare::test1157 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test1179 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test1201 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test1201b PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test1207 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test1227 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test2327 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test2733 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test2733Access PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test3214 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test5711 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test5756Raw PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test5756Wrapped PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test5851 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test2513 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test_OS_non_member PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test_OS_admin_user PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test_bad_share PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test8513 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test8704 PASSED [ 80%] test/integration/test_ishare.py::TestIShare::test13018 PASSED [ 81%] test/integration/test_itimeline.py::TestITimeline::testGeneral PASSED [ 81%] test/integration/test_itimeline.py::TestITimeline::testCollaborativeTimeline PASSED [ 81%] test/integration/test_itimeline.py::TestITimeline::test1173 PASSED [ 81%] test/integration/test_itimeline.py::TestITimeline::test1175 PASSED [ 81%] test/integration/test_itimeline.py::TestITimeline::test3234 PASSED [ 81%] test/integration/test_itypes.py::TestTypes::testGetEnumerationTypes PASSED [ 81%] test/integration/test_itypes.py::TestTypes::testAllEnumerations PASSED [ 81%] test/integration/test_itypes.py::TestTypes::testGetEnumerationWithEntries PASSED [ 81%] test/integration/test_itypes.py::TestTypes::testManageEnumeration PASSED [ 81%] test/integration/test_iupdate.py::TestIUpdate::testSaveArray PASSED [ 81%] test/integration/test_iupdate.py::TestIUpdate::testSaveCollection PASSED [ 81%] test/integration/test_iupdate.py::TestIUpdate::testExternalInfoOnCreation PASSED [ 81%] test/integration/test_iupdate.py::TestIUpdate::testExternalInfoAfterCreationTransient PASSED [ 81%] test/integration/test_iupdate.py::TestIUpdate::testExternalInfoAfterCreationManaged PASSED [ 81%] test/integration/test_iupdate.py::TestIUpdate::testExternalInfoNewInstance PASSED [ 81%] test/integration/test_iupdate.py::TestIUpdate::testExternalInfoNullInstance PASSED [ 81%] test/integration/test_iupdate.py::TestIUpdate::testExternalInfoUpdateInstance PASSED [ 81%] test/integration/test_iupdate.py::TestIUpdate::testCannotSaveDeleted PASSED [ 81%] test/integration/test_librarytest.py::TestLibrary::test9188 PASSED [ 81%] test/integration/test_mail.py::TestMail::testEveryone PASSED [ 82%] test/integration/test_mail.py::TestMail::testUserAdd PASSED [ 82%] test/integration/test_mail.py::TestMail::testComment PASSED [ 82%] test/integration/test_mapannotation.py::TestMapAnnotation::testMapStringField PASSED [ 82%] test/integration/test_mapannotation.py::TestMapAnnotation::testGroupConfigA[data0] PASSED [ 82%] test/integration/test_mapannotation.py::TestMapAnnotation::testGroupConfigA[data1] PASSED [ 82%] test/integration/test_mapannotation.py::TestMapAnnotation::testGroupConfigEdit PASSED [ 82%] test/integration/test_mapannotation.py::TestMapAnnotation::testEmptyItem PASSED [ 82%] test/integration/test_mapannotation.py::TestMapAnnotation::testBigKeys PASSED [ 82%] test/integration/test_metadatastore.py::TestMetadataStore::testBasicUsage PASSED [ 82%] test/integration/test_metadatastore.py::TestMetadataStore::testMetadataService PASSED [ 82%] test/integration/test_model51.py::TestModel51::testExposureTime PASSED [ 82%] test/integration/test_model51.py::TestModel51::testPhysicalSize PASSED [ 82%] test/integration/test_model51.py::TestModel51::testAllLengths[YOTTAMETER] PASSED [ 82%] test/integration/test_model51.py::TestModel51::testAllLengths[ZETTAMETER] PASSED [ 82%] test/integration/test_model51.py::TestModel51::testAllLengths[EXAMETER] PASSED [ 82%] test/integration/test_model51.py::TestModel51::testAllLengths[PETAMETER] PASSED [ 82%] test/integration/test_model51.py::TestModel51::testAllLengths[TERAMETER] PASSED [ 82%] test/integration/test_model51.py::TestModel51::testAllLengths[GIGAMETER] PASSED [ 82%] test/integration/test_model51.py::TestModel51::testAllLengths[MEGAMETER] PASSED [ 82%] test/integration/test_model51.py::TestModel51::testAllLengths[KILOMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[HECTOMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[DECAMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[METER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[DECIMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[CENTIMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[MILLIMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[MICROMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[NANOMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[PICOMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[FEMTOMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[ATTOMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[ZEPTOMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[YOCTOMETER] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[ANGSTROM] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[ASTRONOMICALUNIT] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[LIGHTYEAR] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[PARSEC] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[THOU] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[LINE] PASSED [ 83%] test/integration/test_model51.py::TestModel51::testAllLengths[INCH] PASSED [ 84%] test/integration/test_model51.py::TestModel51::testAllLengths[FOOT] PASSED [ 84%] test/integration/test_model51.py::TestModel51::testAllLengths[YARD] PASSED [ 84%] test/integration/test_model51.py::TestModel51::testAllLengths[MILE] PASSED [ 84%] test/integration/test_model51.py::TestModel51::testAllLengths[POINT] PASSED [ 84%] test/integration/test_model51.py::TestModel51::testAllLengths[PIXEL] PASSED [ 84%] test/integration/test_model51.py::TestModel51::testAllLengths[REFERENCEFRAME] PASSED [ 84%] test/integration/test_model51.py::TestModel51::testAsMapMethod PASSED [ 84%] test/integration/test_model51.py::TestModel51::testMapEagerFetch PASSED [ 84%] test/integration/test_model51.py::TestModel51::testMapSecurity PASSED [ 84%] test/integration/test_model51.py::TestModel51::testUnitProjections PASSED [ 84%] test/integration/test_permissions.py::TestPermissions::testLoginToPublicGroupTicket1940 PASSED [ 84%] test/integration/test_permissions.py::TestPermissions::testLinkingInPrivateGroup PASSED [ 84%] test/integration/test_permissions.py::TestPermissions::testCreatAndUpdatePrivateGroup PASSED [ 84%] test/integration/test_permissions.py::TestPermissions::testCreatAndUpdatePublicGroupReadOnly PASSED [ 84%] test/integration/test_permissions.py::TestPermissions::testCreatAndUpdatePublicGroupReadAnnotate PASSED [ 84%] test/integration/test_permissions.py::TestPermissions::testCreatAndUpdatePublicGroup PASSED [ 84%] test/integration/test_permissions.py::TestPermissions::testCreatGroupAndchangePermissions PASSED [ 84%] test/integration/test_permissions.py::TestPermissions::testGroupOwners PASSED [ 84%] test/integration/test_permissions.py::TestPermissions::testSearchAllGroups PASSED [ 84%] test/integration/test_permissions.py::TestPermissions::testOGContextParameter PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testOGSetImplicitContext PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testOGSetProxyContext PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testOGSetSecurityContext PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testOGArg PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testSaveWithNegOneNotExplicit PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testPrivateGroupCallContext PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testAdminCanQueryWithGroupMinusOneTicket9632 PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testOmeroUserAsAdmin PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testOmeroUserAsNonAdmin PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testImmutablePermissions PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testDisallow PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testClientSet PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testAdminUseOfRawPixelsBean PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testUseOfRawFileBeanScriptReadGroupMinusOne PASSED [ 85%] test/integration/test_permissions.py::TestPermissions::testUseOfRawFileBeanScriptReadCorrectGroup PASSED [ 85%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rw-----admin-admin] PASSED [ 85%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rw-----admin-owner] PASSED [ 85%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rw-----admin-member] PASSED [ 85%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rw-----owner-admin] PASSED [ 85%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rw-----owner-owner] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rw-----owner-member] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rw-----member-admin] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rw-----member-owner] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rw-----member-member] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwr----admin-admin] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwr----admin-owner] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwr----admin-member] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwr----owner-admin] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwr----owner-owner] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwr----owner-member] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwr----member-admin] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwr----member-owner] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwr----member-member] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwra---admin-admin] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwra---admin-owner] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwra---admin-member] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwra---owner-admin] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwra---owner-owner] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwra---owner-member] PASSED [ 86%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwra---member-admin] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwra---member-owner] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwra---member-member] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwrw---admin-admin] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwrw---admin-owner] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwrw---admin-member] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwrw---owner-admin] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwrw---owner-owner] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwrw---owner-member] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwrw---member-admin] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwrw---member-owner] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissionsWorkaround[rwrw---member-member] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rw-----admin-admin] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rw-----admin-owner] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rw-----admin-member] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rw-----owner-admin] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rw-----owner-owner] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rw-----owner-member] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rw-----member-admin] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rw-----member-owner] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rw-----member-member] PASSED [ 87%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwr----admin-admin] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwr----admin-owner] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwr----admin-member] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwr----owner-admin] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwr----owner-owner] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwr----owner-member] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwr----member-admin] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwr----member-owner] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwr----member-member] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwra---admin-admin] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwra---admin-owner] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwra---admin-member] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwra---owner-admin] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwra---owner-owner] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwra---owner-member] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwra---member-admin] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwra---member-owner] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwra---member-member] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwrw---admin-admin] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwrw---admin-owner] PASSED [ 88%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwrw---admin-member] PASSED [ 89%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwrw---owner-admin] PASSED [ 89%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwrw---owner-owner] PASSED [ 89%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwrw---owner-member] PASSED [ 89%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwrw---member-admin] PASSED [ 89%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwrw---member-owner] PASSED [ 89%] test/integration/test_permissions.py::TestPermissionProjections::testProjectionPermissions[rwrw---member-member] PASSED [ 89%] test/integration/test_permissions.py::TestPermissionProjections::testExtendedRestrictions[PlateI] SKIPPED [ 89%] test/integration/test_permissions.py::TestPermissionProjections::testExtendedRestrictions[WellI] SKIPPED [ 89%] test/integration/test_permissions.py::TestPermissionProjections::testExtendedRestrictions[ImageI] SKIPPED [ 89%] test/integration/test_permissions.py::TestPermissionProjections::testExtendedRestrictions[FileAnnotationI] SKIPPED [ 89%] test/integration/test_pixelsService.py::TestPixelsService::test9655 PASSED [ 89%] test/integration/test_rawfilestore.py::TestRFS::testNullSize11743 PASSED [ 89%] test/integration/test_rawfilestore.py::TestRFS::testGetFileId PASSED [ 89%] test/integration/test_rawpixelsstore.py::TestRPS::testTicket4737WithClose PASSED [ 89%] test/integration/test_rawpixelsstore.py::TestRPS::testTicket4737WithSave PASSED [ 89%] test/integration/test_rawpixelsstore.py::TestRPS::testTicket4737WithForEachTile PASSED [ 89%] test/integration/test_rawpixelsstore.py::TestRPS::testBigPlane PASSED [ 89%] test/integration/test_rawpixelsstore.py::TestRPS::testRomioToPyramid PASSED [ 89%] test/integration/test_rawpixelsstore.py::TestRPS::test2RomioToPyramidWithNegOne PASSED [ 89%] test/integration/test_rawpixelsstore.py::TestRPS::testPyramidConcurrentAccess PASSED [ 90%] test/integration/test_rawpixelsstore.py::TestTiles::testTiles PASSED [ 90%] test/integration/test_reimport.py::TestReimportArchivedFiles::testConvertSynthetic PASSED [ 90%] test/integration/test_render.py::TestRendering::test_render_region PASSED [ 90%] test/integration/test_reporawfilestore.py::TestRepoRawFileStore::testCreate PASSED [ 90%] test/integration/test_reporawfilestore.py::TestRepoRawFileStore::testWrite PASSED [ 90%] test/integration/test_reporawfilestore.py::TestRepoRawFileStore::testFailedWrite PASSED [ 90%] test/integration/test_reporawfilestore.py::TestRepoRawFileStore::testWriteRead PASSED [ 90%] test/integration/test_reporawfilestore.py::TestRepoRawFileStore::testAppend PASSED [ 90%] test/integration/test_reporawfilestore.py::TestRepoRawFileStore::testTruncateToZero PASSED [ 90%] test/integration/test_reporawfilestore.py::TestRepoRawFileStore::testClose PASSED [ 90%] test/integration/test_reporawfilestore.py::TestRepoRawFileStore::testImportLogFilenameSetting PASSED [ 90%] test/integration/test_repository.py::TestRepository::testBasicUsage PASSED [ 90%] test/integration/test_repository.py::TestRepository::testSanityCheckRepos PASSED [ 90%] test/integration/test_repository.py::TestRepository::testManagedRepoAsPubliRepo PASSED [ 90%] test/integration/test_repository.py::TestFileExists::testFileExistsForDirectory PASSED [ 90%] test/integration/test_repository.py::TestFileExists::testFileExistsForFile PASSED [ 90%] test/integration/test_repository.py::TestManagedRepositoryMultiUser::testTopPrivateGroup PASSED [ 90%] test/integration/test_repository.py::TestManagedRepositoryMultiUser::testDirPrivateGroup PASSED [ 90%] test/integration/test_repository.py::TestManagedRepositoryMultiUser::testDirReadOnlyGroup PASSED [ 90%] test/integration/test_repository.py::TestManagedRepositoryMultiUser::testDirReadWriteGroup PASSED [ 91%] test/integration/test_repository.py::TestManagedRepositoryMultiUser::testDirReadAnnotateGroup PASSED [ 91%] test/integration/test_repository.py::TestManagedRepositoryMultiUser::testMultiGroup PASSED [ 91%] test/integration/test_repository.py::TestPythonImporter::testImportFileset PASSED [ 91%] test/integration/test_repository.py::TestPythonImporter::testImportPaths PASSED [ 91%] test/integration/test_repository.py::TestPythonImporter::testReopenRawFileStoresPR2542 PASSED [ 91%] test/integration/test_repository.py::TestPythonImporter::testImportsFrom2Groups PASSED [ 91%] test/integration/test_repository.py::TestRawAccess::testAsNonAdmin PASSED [ 91%] test/integration/test_repository.py::TestRawAccess::testAsAdmin PASSED [ 91%] test/integration/test_repository.py::TestDbSync::testMtime PASSED [ 91%] test/integration/test_repository.py::TestDbSync::testFileExists PASSED [ 91%] test/integration/test_repository.py::TestDbSync::testNonDbFileNotReturned PASSED [ 91%] test/integration/test_repository.py::TestRecursiveDelete::testCmdDeleteCantDeleteDirectories PASSED [ 91%] test/integration/test_repository.py::TestRecursiveDelete::testRecursiveDeleteMethodAvailable PASSED [ 91%] test/integration/test_repository.py::TestRecursiveDelete::testDoubleDot PASSED [ 91%] test/integration/test_repository.py::TestDeleteLog::testSimpleDelete PASSED [ 91%] test/integration/test_repository.py::TestUserTemplate::testCreateUuidFails PASSED [ 91%] test/integration/test_repository.py::TestUserTemplate::testCreateUserDirPasses PASSED [ 91%] test/integration/test_repository.py::TestUserTemplate::testCreateUuidUnderUserDirPasses PASSED [ 91%] test/integration/test_repository.py::TestUserTemplate::testUserDirShouldBeGloballyWriteable PASSED [ 91%] test/integration/test_repository.py::TestFilesetQueries::testDeleteQuery PASSED [ 92%] test/integration/test_repository.py::TestFilesetQueries::testCountFilesetFiles PASSED [ 92%] test/integration/test_repository.py::TestFilesetQueries::testImportedImageFiles PASSED [ 92%] test/integration/test_repository.py::TestOriginalMetadata::testFakeImport PASSED [ 92%] test/integration/test_repository.py::TestDeletePerformance::testImport PASSED [ 92%] test/integration/test_rois.py::TestRois::teststats1 PASSED [ 92%] test/integration/test_rois.py::TestRois::test3703 PASSED [ 92%] test/integration/test_rois.py::TestRois::testGetROICount PASSED [ 92%] test/integration/test_rois.py::TestRois::test8990 PASSED [ 92%] test/integration/test_rois.py::TestRois::testShapeColors[color0] PASSED [ 92%] test/integration/test_rois.py::TestRois::testShapeColors[color1] PASSED [ 92%] test/integration/test_rois.py::TestRois::testShapeColors[color2] PASSED [ 92%] test/integration/test_rois.py::TestRois::testShapeColors[color3] PASSED [ 92%] test/integration/test_rois.py::TestRois::testShapeColors[color4] PASSED [ 92%] test/integration/test_rois.py::TestRois::testShapeColors[color5] PASSED [ 92%] test/integration/test_rois.py::TestRois::testShapeColors[color6] PASSED [ 92%] test/integration/test_rois.py::TestRois::testShapeColors[color7] PASSED [ 92%] test/integration/test_rois.py::TestRois::testShapeColors[color8] PASSED [ 92%] test/integration/test_rois.py::TestRois::testShapeColors[color9] PASSED [ 92%] test/integration/test_rois.py::TestRois::testGetShapeStatsRestricted PASSED [ 92%] test/integration/test_scripts.py::TestScripts::testBasicUsage PASSED [ 93%] test/integration/test_scripts.py::TestScripts::testTicket1036 PASSED [ 93%] test/integration/test_scripts.py::TestScripts::testUploadAndPing PASSED [ 93%] test/integration/test_scripts.py::TestScripts::testUpload2562 PASSED [ 93%] test/integration/test_scripts.py::TestScripts::testDelete6905 PASSED [ 93%] test/integration/test_scripts.py::TestScripts::testDelete11371 PASSED [ 93%] test/integration/test_scripts.py::TestScripts::testUploadOfficialScript PASSED [ 93%] test/integration/test_scripts.py::TestScripts::testRunScript PASSED [ 93%] test/integration/test_scripts.py::TestScripts::testEditScript PASSED [ 93%] test/integration/test_scripts.py::TestScripts::testScriptValidation PASSED [ 93%] test/integration/test_scripts.py::TestScripts::testSpeedOfThumbnailFigure PASSED [ 93%] test/integration/test_scripts.py::TestScripts::test6066 PASSED [ 93%] test/integration/test_scripts.py::TestScripts::testDynamicTime PASSED [ 93%] test/integration/test_scripts.py::TestScripts::testDynamicUpdate PASSED [ 93%] test/integration/test_search.py::TestSearch::test2541 PASSED [ 93%] test/integration/test_search.py::TestSearch::test3164Private PASSED [ 93%] test/integration/test_search.py::TestSearch::test3164ReadOnlySelf PASSED [ 93%] test/integration/test_search.py::TestSearch::test3164ReadOnlyOther PASSED [ 93%] test/integration/test_search.py::TestSearch::test3164CollabSelf PASSED [ 93%] test/integration/test_search.py::TestSearch::test3164CollabOther PASSED [ 93%] test/integration/test_search.py::TestSearch::test3721Ordering PASSED [ 94%] test/integration/test_search.py::TestSearch::test8692 PASSED [ 94%] test/integration/test_search.py::TestSearch::test8846 PASSED [ 94%] test/integration/test_search.py::TestSearch::testClientPath PASSED [ 94%] test/integration/test_search.py::TestSearch::testFilename PASSED [ 94%] test/integration/test_search.py::TestSearch::test_csv_attachment PASSED [ 94%] test/integration/test_search.py::TestSearch::test_txt_attachment PASSED [ 94%] test/integration/test_search.py::TestSearch::test_word_portions PASSED [ 94%] test/integration/test_search.py::TestSearch::test_empty_query_string PASSED [ 94%] test/integration/test_search.py::TestSearch::test_hyphen_underscore[very-small-very small] PASSED [ 94%] test/integration/test_search.py::TestSearch::test_hyphen_underscore[very-small-very-small] PASSED [ 94%] test/integration/test_search.py::TestSearch::test_hyphen_underscore[very-small-very_small] PASSED [ 94%] test/integration/test_search.py::TestSearch::test_hyphen_underscore[very-small-small very] PASSED [ 94%] test/integration/test_search.py::TestSearch::test_hyphen_underscore[very_small-very small] PASSED [ 94%] test/integration/test_search.py::TestSearch::test_hyphen_underscore[very_small-very-small] PASSED [ 94%] test/integration/test_search.py::TestSearch::test_hyphen_underscore[very_small-very_small] PASSED [ 94%] test/integration/test_search.py::TestSearch::test_hyphen_underscore[very_small-small very] PASSED [ 94%] test/integration/test_search.py::TestSearch::test_hyphen_underscore[very small-very small] PASSED [ 94%] test/integration/test_search.py::TestSearch::test_hyphen_underscore[very small-very-small] PASSED [ 94%] test/integration/test_search.py::TestSearch::test_hyphen_underscore[very small-very_small] PASSED [ 94%] test/integration/test_search.py::TestSearch::test_hyphen_underscore[very small-small very] PASSED [ 95%] test/integration/test_search.py::TestSearch::test_map_annotations PASSED [ 95%] test/integration/test_simple.py::TestSimple::testUserId PASSED [ 95%] test/integration/test_simple.py::TestSimple::testGroupId PASSED [ 95%] test/integration/test_simple.py::TestSimple::testGroupPermissions PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testThumbs PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test9070 PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testPrivate10618RootWithGrpCtx PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testPrivate10618RootWithGrpCtxButNoLoad PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testReadOnly10618RootWithGrpCtx PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testReadOnly10618RootWithGrpCtxButNoLoad PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testReadOnly10618MemberWithGrpCtxButNoLoad PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsThumbs PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsThumbsReadOnly PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readOnly-saveCurrent] PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readOnly-saveAs] PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readOnly-request] PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readOnly-resetDefault] PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readOnly-resetDefaultNoSave] PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readAnnotate-saveCurrent] PASSED [ 95%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readAnnotate-saveAs] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readAnnotate-request] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readAnnotate-resetDefault] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readAnnotate-resetDefaultNoSave] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readWrite-saveCurrent] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readWrite-saveAs] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readWrite-request] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readWrite-resetDefault] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[owner-readWrite-resetDefaultNoSave] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readOnly-saveCurrent] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readOnly-saveAs] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readOnly-request] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readOnly-resetDefault] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readOnly-resetDefaultNoSave] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readAnnotate-saveCurrent] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readAnnotate-saveAs] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readAnnotate-request] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readAnnotate-resetDefault] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readAnnotate-resetDefaultNoSave] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readWrite-saveCurrent] PASSED [ 96%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readWrite-saveAs] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readWrite-request] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readWrite-resetDefault] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsRnd[admin-readWrite-resetDefaultNoSave] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsGetThumbnail[readOnly-owner] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsGetThumbnail[readOnly-admin] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsGetThumbnail[readAnnotate-owner] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsGetThumbnail[readAnnotate-admin] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsGetThumbnail[readWrite-owner] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsGetThumbnail[readWrite-admin] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsSetRnd[readOnly-owner] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsSetRnd[readOnly-admin] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsSetRnd[readAnnotate-owner] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsSetRnd[readAnnotate-admin] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsSetRnd[readWrite-owner] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::test12145ShareSettingsSetRnd[readWrite-admin] PASSED [ 97%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testGetThumbnailSetAfterApplySettings PASSED [ 97%] test/integration/test_thumbs.py::TestThumbs::testCreateThumbnails PASSED [ 97%] test/integration/test_thumbs.py::TestThumbs::testCreateThumbnails64x64 PASSED [ 97%] test/integration/test_thumbs.py::TestThumbs::testCreateThumbnailsByLongestSideSet64x64 PASSED [ 97%] test/integration/test_thumbs.py::TestThumbs::testThumbnailExists PASSED [ 98%] test/integration/test_thumbs.py::TestThumbs::testThumbnailVersion[one] PASSED [ 98%] test/integration/test_thumbs.py::TestThumbs::testThumbnailVersion[set] PASSED [ 98%] test/integration/test_thumbs.py::TestThumbs::testGetThumbnailx64x64 PASSED [ 98%] test/integration/test_thumbs.py::TestThumbs::testGetThumbnailByLongestSidex64 PASSED [ 98%] test/integration/test_thumbs.py::TestThumbs::testGetThumbnailDirectx64x64 PASSED [ 98%] test/integration/test_thumbs.py::TestThumbs::testGetThumbnailForSectionDirectx0x0x64x64 PASSED [ 98%] test/integration/test_thumbs.py::TestThumbs::testGetThumbnailx64x60 PASSED [ 98%] test/integration/test_thumbs.py::TestThumbs::testGetThumbnailByLongestSidex60 PASSED [ 98%] test/integration/test_thumbs.py::TestThumbs::testGetThumbnailDirectx64x60 PASSED [ 98%] test/integration/test_thumbs.py::TestThumbs::testGetThumbnailForSectionDirectx0x0x64x60 PASSED [ 98%] test/integration/test_thumbs.py::TestThumbs::testGetThumbnailSetx64x64 PASSED [ 98%] test/integration/test_thumbs.py::TestThumbs::testGetThumbnailByLongestSideSetx64 PASSED [ 98%] test/integration/test_tickets1000.py::TestTicket1000::test711 PASSED [ 98%] test/integration/test_tickets1000.py::TestTicket1000::test843 PASSED [ 98%] test/integration/test_tickets1000.py::TestTicket1000::test880 PASSED [ 98%] test/integration/test_tickets1000.py::TestTicket1000::test883WithoutClose PASSED [ 98%] test/integration/test_tickets1000.py::TestTicket1000::test883WithClose PASSED [ 98%] test/integration/test_tickets1000.py::TestTicket1000::test883Upload PASSED [ 98%] test/integration/test_tickets1000.py::TestTicket1000::test985 PASSED [ 98%] test/integration/test_tickets2000.py::TestTickets2000::test1064 PASSED [ 99%] test/integration/test_tickets2000.py::TestTickets2000::test1067 PASSED [ 99%] test/integration/test_tickets2000.py::TestTickets2000::test1027 PASSED [ 99%] test/integration/test_tickets2000.py::TestTickets2000::test1069 PASSED [ 99%] test/integration/test_tickets2000.py::TestTickets2000::test1071 PASSED [ 99%] test/integration/test_tickets2000.py::TestTickets2000::test1071_1 PASSED [ 99%] test/integration/test_tickets2000.py::TestTickets2000::test1072 PASSED [ 99%] test/integration/test_tickets2000.py::TestTickets2000::test1088 PASSED [ 99%] test/integration/test_tickets2000.py::TestTickets2000::test1109 PASSED [ 99%] test/integration/test_tickets2000.py::TestTickets2000::test1163 PASSED [ 99%] test/integration/test_tickets2000.py::TestTickets2000::test1183 PASSED [ 99%] test/integration/test_tickets3000.py::TestTickets3000::test2396 PASSED [ 99%] test/integration/test_tickets3000.py::TestTickets3000::test2547 PASSED [ 99%] test/integration/test_tickets3000.py::TestTickets3000::test2628 PASSED [ 99%] test/integration/test_tickets3000.py::TestTickets3000::test2952 PASSED [ 99%] test/integration/test_tickets3000.py::TestTickets3000::test2762 PASSED [ 99%] test/integration/test_tickets4000.py::TestTickets4000::testChangeActiveGroup PASSED [ 99%] test/integration/test_tickets4000.py::TestTickets4000::testChangeActiveGroupWhenConnectionLost PASSED [ 99%] test/integration/test_tickets4000.py::TestTickets4000::test3201 PASSED [ 99%] test/integration/test_tickets4000.py::TestTickets4000::test3131 PASSED [ 99%] test/integration/test_util.py::TestUpgradeCheck::testReal PASSED [100%] ==================================== ERRORS ==================================== ______________ ERROR at setup of TestConnectionMethods.testClose _______________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k df58f488-065b-4f48-9290-b78bef6a1c78 -p 14064 import -d 1025 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:34:47,802 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:34:47,817 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:34:47,865 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:34:47,866 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:34:48,178 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:34:48,319 770 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (141ms total) [0 unknowns]\n2025-12-09 02:34:48,351 802 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:34:48,711 1162 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:34:48,917 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:34:48,923 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:34:48,923 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:34:48,923 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:34:48,923 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:34:48,923 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:34:48,923 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:34:49,261 1712 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1025\n2025-12-09 02:34:49,273 1724 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1025\n2025-12-09 02:34:49,276 1727 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:34:49,455 1906 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:34:49,465 1916 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:34:49,476 1927 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:34:49,485 1936 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:34:49,490 1941 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:34:49,500 1951 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:34:49,509 1960 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:34:49,544 1995 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:34:49,584 2035 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4608\n2025-12-09 02:34:49,596 2047 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:34:49,599 2050 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:34:49,599 2050 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.582\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:34:44,103 INFO [ omero.gateway] (MainThread) created connection (uuid=e2266f70-4e70-4253-a358-c01d6d42ae55) I2025-12-09 02:34:44,162 INFO [ omero.gateway] (MainThread) created connection (uuid=df58f488-065b-4f48-9290-b78bef6a1c78) 2025-12-09 02:34:49,739 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=e2266f70-4e70-4253-a358-c01d6d42ae55) INFO omero.gateway:__init__.py:2307 created connection (uuid=df58f488-065b-4f48-9290-b78bef6a1c78) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _________ ERROR at setup of TestConnectionMethods.testTopLevelObjects __________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 7b51f732-a86b-4f01-b3a7-0b69659a2adf -p 14064 import -d 1025 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:34:54,397 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:34:54,412 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:34:54,459 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:34:54,460 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:34:54,765 610 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:34:54,904 749 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (139ms total) [0 unknowns]\n2025-12-09 02:34:54,936 781 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:34:55,302 1147 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:34:55,511 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:34:55,521 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:34:55,521 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:34:55,521 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:34:55,521 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:34:55,521 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:34:55,521 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:34:55,853 1698 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1025\n2025-12-09 02:34:55,866 1711 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1025\n2025-12-09 02:34:55,869 1714 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:34:56,021 1866 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:34:56,031 1876 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:34:56,044 1889 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:34:56,054 1899 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:34:56,059 1904 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:34:56,068 1913 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:34:56,078 1923 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:34:56,127 1972 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:34:56,169 2014 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4612\n2025-12-09 02:34:56,180 2025 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:34:56,182 2027 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:34:56,182 2027 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.570\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:34:49,821 INFO [ omero.gateway] (MainThread) created connection (uuid=6df4b70f-7cdd-4394-8d7b-9960ae3a8110) I2025-12-09 02:34:49,880 INFO [ omero.gateway] (MainThread) created connection (uuid=7b51f732-a86b-4f01-b3a7-0b69659a2adf) 2025-12-09 02:34:56,334 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=6df4b70f-7cdd-4394-8d7b-9960ae3a8110) INFO omero.gateway:__init__.py:2307 created connection (uuid=7b51f732-a86b-4f01-b3a7-0b69659a2adf) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) __________________ ERROR at setup of TestImage.testThumbnail ___________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 2af7e97b-f9cf-429f-a9c9-1e9d99309143 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:36:23,752 254 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:36:23,768 270 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:36:23,817 319 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:36:23,818 320 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:36:24,131 633 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:36:24,280 782 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 147ms. (149ms total) [0 unknowns]\n2025-12-09 02:36:24,313 815 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:36:24,685 1187 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:36:24,889 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:36:24,899 1401 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:36:24,900 1402 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:36:24,900 1402 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:36:24,900 1402 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:36:24,900 1402 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:36:24,900 1402 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:36:25,246 1748 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:36:25,260 1762 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:36:25,263 1765 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:36:25,435 1937 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:36:25,445 1947 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:36:25,458 1960 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:36:25,541 2043 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:36:25,546 2048 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:36:25,557 2059 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:36:25,566 2068 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:36:25,601 2103 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:36:25,644 2146 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4704\n2025-12-09 02:36:25,663 2165 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:36:25,666 2168 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:36:25,666 2168 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.669\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:36:18,154 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:36:18,158 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:36:18,192 INFO [ omero.gateway] (MainThread) created connection (uuid=aede3885-8f51-4e2e-88a5-e0fc0f47c56a) 2025-12-09 02:36:18,622 INFO [ omero.gateway] (MainThread) created connection (uuid=643b4c85-c7ad-4893-bb8c-c3c746d078dc) 2025-12-09 02:36:18,658 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:36:18,692 INFO [ omero.gateway] (MainThread) created connection (uuid=18aa3a0f-9366-4e9e-bb2d-e9860fb243f3) 2025-12-09 02:36:18,726 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:36:18,759 INFO [ omero.gateway] (MainThread) created connection (uuid=56b1f53e-8b91-4a4e-a691-2da8fc32fb07) 2025-12-09 02:36:18,798 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:36:18,830 INFO [ omero.gateway] (MainThread) created connection (uuid=474744c2-2c2d-4dcd-b79b-9d65b5858db6) 2025-12-09 02:36:18,869 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:36:18,902 INFO [ omero.gateway] (MainThread) created connection (uuid=5d4464ff-0392-427b-a58a-208e46866e30) 2025-12-09 02:36:18,939 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:36:18,971 INFO [ omero.gateway] (MainThread) created connection (uuid=ed7aaeb6-3738-4886-83b0-2158c292c8e1) 2025-12-09 02:36:19,006 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:36:19,039 INFO [ omero.gateway] (MainThread) created connection (uuid=ececf937-6d49-4915-8b3c-980b7c7badb6) 2025-12-09 02:36:19,084 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:36:19,116 INFO [ omero.gateway] (MainThread) created connection (uuid=14648ede-e6f2-4266-ac10-f1ed608a06ec) 2025-12-09 02:36:19,164 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:36:19,198 INFO [ omero.gateway] (MainThread) created connection (uuid=9e513759-ba33-4f7d-874f-adaf263685de) 2025-12-09 02:36:19,242 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:36:19,245 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:36:19,279 INFO [ omero.gateway] (MainThread) created connection (uuid=23e7484d-cfba-4127-a07a-46a3a7e0b7da) 2025-12-09 02:36:19,345 INFO [ omero.gateway] (MainThread) created connection (uuid=f4fbf2d0-6182-4660-88ce-2b7d3c3e9a17) I2025-12-09 02:36:19,407 INFO [ omero.gateway] (MainThread) created connection (uuid=2af7e97b-f9cf-429f-a9c9-1e9d99309143) 2025-12-09 02:36:25,812 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=aede3885-8f51-4e2e-88a5-e0fc0f47c56a) INFO omero.gateway:__init__.py:2307 created connection (uuid=643b4c85-c7ad-4893-bb8c-c3c746d078dc) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=18aa3a0f-9366-4e9e-bb2d-e9860fb243f3) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=56b1f53e-8b91-4a4e-a691-2da8fc32fb07) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=474744c2-2c2d-4dcd-b79b-9d65b5858db6) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=5d4464ff-0392-427b-a58a-208e46866e30) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=ed7aaeb6-3738-4886-83b0-2158c292c8e1) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=ececf937-6d49-4915-8b3c-980b7c7badb6) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=14648ede-e6f2-4266-ac10-f1ed608a06ec) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=9e513759-ba33-4f7d-874f-adaf263685de) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=23e7484d-cfba-4127-a07a-46a3a7e0b7da) INFO omero.gateway:__init__.py:2307 created connection (uuid=f4fbf2d0-6182-4660-88ce-2b7d3c3e9a17) INFO omero.gateway:__init__.py:2307 created connection (uuid=2af7e97b-f9cf-429f-a9c9-1e9d99309143) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _________________ ERROR at setup of TestImage.testThumbnailSet _________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 0acf3b85-37cc-418f-aa8b-e9693eed4f09 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:36:30,542 243 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:36:30,557 258 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:36:30,604 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:36:30,605 306 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:36:30,910 611 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:36:31,047 748 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 135ms. (137ms total) [0 unknowns]\n2025-12-09 02:36:31,078 779 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:36:31,438 1139 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:36:31,642 1343 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:36:31,647 1348 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:36:31,647 1348 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:36:31,647 1348 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:36:31,647 1348 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:36:31,648 1349 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:36:31,648 1349 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:36:31,974 1675 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:36:31,986 1687 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:36:31,989 1690 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:36:32,152 1853 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:36:32,162 1863 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:36:32,173 1874 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:36:32,182 1883 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:36:32,187 1888 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:36:32,197 1898 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:36:32,206 1907 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:36:32,240 1941 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:36:32,278 1979 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4708\n2025-12-09 02:36:32,288 1989 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:36:32,291 1992 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:36:32,291 1992 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.555\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:36:25,897 INFO [ omero.gateway] (MainThread) created connection (uuid=ad041ac6-649e-4b6d-8fac-62e89274b605) I2025-12-09 02:36:25,959 INFO [ omero.gateway] (MainThread) created connection (uuid=0acf3b85-37cc-418f-aa8b-e9693eed4f09) 2025-12-09 02:36:32,443 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=ad041ac6-649e-4b6d-8fac-62e89274b605) INFO omero.gateway:__init__.py:2307 created connection (uuid=0acf3b85-37cc-418f-aa8b-e9693eed4f09) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _______________ ERROR at setup of TestImage.testRenderingModels ________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k af90d1d4-3ae1-4e4c-a458-9dba381d296b -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:36:36,206 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:36:36,221 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:36:36,269 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:36:36,270 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:36:36,572 607 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:36:36,708 743 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (136ms total) [0 unknowns]\n2025-12-09 02:36:36,739 774 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:36:37,090 1125 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:36:37,287 1322 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:36:37,292 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:36:37,292 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:36:37,292 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:36:37,292 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:36:37,292 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:36:37,292 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:36:37,627 1662 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:36:37,640 1675 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:36:37,643 1678 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:36:37,798 1833 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:36:37,808 1843 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:36:37,819 1854 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:36:37,828 1863 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:36:37,833 1868 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:36:37,842 1877 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:36:37,852 1887 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:36:37,878 1913 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:36:37,917 1952 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4712\n2025-12-09 02:36:37,928 1963 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:36:37,931 1966 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:36:37,931 1966 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.545\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:36:32,527 INFO [ omero.gateway] (MainThread) created connection (uuid=d33f77fc-ff82-438d-a8ce-74cb391a36ed) I2025-12-09 02:36:32,589 INFO [ omero.gateway] (MainThread) created connection (uuid=af90d1d4-3ae1-4e4c-a458-9dba381d296b) 2025-12-09 02:36:38,075 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=d33f77fc-ff82-438d-a8ce-74cb391a36ed) INFO omero.gateway:__init__.py:2307 created connection (uuid=af90d1d4-3ae1-4e4c-a458-9dba381d296b) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _________________ ERROR at setup of TestImage.testSplitChannel _________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 9cb871d0-2824-4599-ad09-0dcfbead3345 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:36:42,677 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:36:42,692 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:36:42,739 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:36:42,740 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:36:43,039 603 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:36:43,176 740 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (137ms total) [0 unknowns]\n2025-12-09 02:36:43,207 771 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:36:43,560 1124 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:36:43,759 1323 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:36:43,763 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:36:43,763 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:36:43,763 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:36:43,763 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:36:43,763 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:36:43,763 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:36:44,103 1667 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:36:44,115 1679 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:36:44,118 1682 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:36:44,258 1822 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:36:44,268 1832 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:36:44,279 1843 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:36:44,289 1853 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:36:44,293 1857 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:36:44,303 1867 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:36:44,312 1876 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:36:44,337 1901 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:36:44,375 1939 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4716\n2025-12-09 02:36:44,389 1953 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:36:44,392 1956 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:36:44,392 1956 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.529\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:36:38,156 INFO [ omero.gateway] (MainThread) created connection (uuid=6c5b7ef3-fc66-43bc-a3e6-5255be616b70) I2025-12-09 02:36:38,216 INFO [ omero.gateway] (MainThread) created connection (uuid=9cb871d0-2824-4599-ad09-0dcfbead3345) 2025-12-09 02:36:44,548 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=6c5b7ef3-fc66-43bc-a3e6-5255be616b70) INFO omero.gateway:__init__.py:2307 created connection (uuid=9cb871d0-2824-4599-ad09-0dcfbead3345) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) __________________ ERROR at setup of TestImage.testLinePlots ___________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 2ebb098f-9955-488f-be77-96e1e9703155 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:36:48,934 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:36:48,949 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:36:48,997 313 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:36:48,998 314 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:36:49,307 623 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:36:49,447 763 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (140ms total) [0 unknowns]\n2025-12-09 02:36:49,479 795 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:36:49,840 1156 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:36:50,041 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:36:50,046 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:36:50,046 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:36:50,046 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:36:50,046 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:36:50,046 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:36:50,046 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:36:50,386 1702 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:36:50,398 1714 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:36:50,401 1717 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:36:50,551 1867 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:36:50,561 1877 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:36:50,571 1887 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:36:50,580 1896 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:36:50,585 1901 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:36:50,595 1911 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:36:50,604 1920 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:36:50,630 1946 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:36:50,669 1985 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4720\n2025-12-09 02:36:50,678 1994 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:36:50,681 1997 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:36:50,681 1997 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.536\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:36:44,632 INFO [ omero.gateway] (MainThread) created connection (uuid=a3ec5ca9-bc24-4456-aeb4-cfd0091a3d59) I2025-12-09 02:36:44,694 INFO [ omero.gateway] (MainThread) created connection (uuid=2ebb098f-9955-488f-be77-96e1e9703155) 2025-12-09 02:36:50,833 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=a3ec5ca9-bc24-4456-aeb4-cfd0091a3d59) INFO omero.gateway:__init__.py:2307 created connection (uuid=2ebb098f-9955-488f-be77-96e1e9703155) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _________________ ERROR at setup of TestImage.testProjections __________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 1a045360-d430-4e8e-88ab-a13d442c9337 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:36:55,312 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:36:55,327 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:36:55,376 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:36:55,377 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:36:55,687 627 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:36:55,828 768 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (141ms total) [0 unknowns]\n2025-12-09 02:36:55,860 800 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:36:56,224 1164 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:36:56,437 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:36:56,442 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:36:56,442 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:36:56,442 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:36:56,442 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:36:56,442 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:36:56,442 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:36:56,780 1720 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:36:56,793 1733 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:36:56,796 1736 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:36:56,936 1876 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:36:56,946 1886 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:36:56,957 1897 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:36:56,966 1906 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:36:56,971 1911 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:36:56,982 1922 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:36:56,991 1931 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:36:57,017 1957 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:36:57,055 1995 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4724\n2025-12-09 02:36:57,065 2005 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:36:57,067 2007 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:36:57,067 2007 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.530\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:36:50,918 INFO [ omero.gateway] (MainThread) created connection (uuid=308b61b5-b275-4c26-aedc-4007ab5ff203) I2025-12-09 02:36:50,978 INFO [ omero.gateway] (MainThread) created connection (uuid=1a045360-d430-4e8e-88ab-a13d442c9337) 2025-12-09 02:36:57,218 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=308b61b5-b275-4c26-aedc-4007ab5ff203) INFO omero.gateway:__init__.py:2307 created connection (uuid=1a045360-d430-4e8e-88ab-a13d442c9337) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) __________________ ERROR at setup of TestImage.testProperties __________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 57546d13-1d01-4603-8cce-0f341e1ac0f8 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:37:01,741 256 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:37:01,756 271 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:37:01,808 323 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:37:01,809 324 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:37:02,126 641 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:37:02,269 784 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (143ms total) [0 unknowns]\n2025-12-09 02:37:02,302 817 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:37:02,675 1190 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:37:02,882 1397 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:37:02,887 1402 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:37:02,887 1402 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:37:02,887 1402 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:37:02,887 1402 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:37:02,887 1402 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:37:02,887 1402 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:37:03,238 1753 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:37:03,251 1766 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:37:03,254 1769 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:37:03,398 1913 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:37:03,408 1923 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:37:03,418 1933 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:03,429 1944 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:03,434 1949 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:37:03,443 1958 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:03,452 1967 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:03,481 1996 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:37:03,523 2038 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4728\n2025-12-09 02:37:03,534 2049 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:03,537 2052 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:03,537 2052 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.548\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:36:57,303 INFO [ omero.gateway] (MainThread) created connection (uuid=097b61ff-6e9e-4768-ad3e-3fbdcb2e8f18) I2025-12-09 02:36:57,364 INFO [ omero.gateway] (MainThread) created connection (uuid=57546d13-1d01-4603-8cce-0f341e1ac0f8) 2025-12-09 02:37:03,677 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=097b61ff-6e9e-4768-ad3e-3fbdcb2e8f18) INFO omero.gateway:__init__.py:2307 created connection (uuid=57546d13-1d01-4603-8cce-0f341e1ac0f8) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ________________ ERROR at setup of TestImage.testPixelSizeUnits ________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 43fbfd37-6a96-48d4-912f-b89217a77451 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:37:07,549 254 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:37:07,564 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:37:07,613 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:37:07,615 320 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:37:07,926 631 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:37:08,068 773 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (141ms total) [0 unknowns]\n2025-12-09 02:37:08,099 804 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:37:08,455 1160 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:37:08,658 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:37:08,664 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:37:08,664 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:37:08,664 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:37:08,664 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:37:08,664 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:37:08,664 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:37:09,007 1712 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:37:09,019 1724 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:37:09,022 1727 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:37:09,164 1869 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:37:09,174 1879 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:37:09,184 1889 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:09,193 1898 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:09,198 1903 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:37:09,208 1913 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:09,217 1922 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:09,245 1950 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:37:09,286 1991 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4732\n2025-12-09 02:37:09,294 1999 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:09,297 2002 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:09,297 2002 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.539\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:37:03,762 INFO [ omero.gateway] (MainThread) created connection (uuid=38ca1848-5150-41b6-94ca-2013d10757de) I2025-12-09 02:37:03,821 INFO [ omero.gateway] (MainThread) created connection (uuid=43fbfd37-6a96-48d4-912f-b89217a77451) 2025-12-09 02:37:09,449 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=38ca1848-5150-41b6-94ca-2013d10757de) INFO omero.gateway:__init__.py:2307 created connection (uuid=43fbfd37-6a96-48d4-912f-b89217a77451) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ________________ ERROR at setup of TestImage.testUnitsGetValue _________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k bd48c3f5-2826-490c-b89d-8108890e5e3c -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:37:14,134 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:37:14,149 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:37:14,197 315 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:37:14,198 316 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:37:14,507 625 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:37:14,647 765 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (140ms total) [0 unknowns]\n2025-12-09 02:37:14,678 796 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:37:15,037 1155 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:37:15,240 1358 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:37:15,245 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:37:15,245 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:37:15,245 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:37:15,245 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:37:15,245 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:37:15,245 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:37:15,592 1710 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:37:15,605 1723 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:37:15,608 1726 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:37:15,743 1861 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:37:15,753 1871 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:37:15,763 1881 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:15,772 1890 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:15,777 1895 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:37:15,787 1905 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:15,796 1914 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:15,822 1940 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:37:15,864 1982 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4736\n2025-12-09 02:37:15,875 1993 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:15,878 1996 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:15,878 1996 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.534\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:37:09,531 INFO [ omero.gateway] (MainThread) created connection (uuid=7f8981cb-903b-4dc7-952c-4c2091920c54) I2025-12-09 02:37:09,589 INFO [ omero.gateway] (MainThread) created connection (uuid=bd48c3f5-2826-490c-b89d-8108890e5e3c) 2025-12-09 02:37:16,024 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=7f8981cb-903b-4dc7-952c-4c2091920c54) INFO omero.gateway:__init__.py:2307 created connection (uuid=bd48c3f5-2826-490c-b89d-8108890e5e3c) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ____________ ERROR at setup of TestImage.testChannelWavelengthUnits ____________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k a9f28902-fe5e-45f1-a10c-a7ef3f9db1c8 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:37:20,430 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:37:20,445 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:37:20,495 315 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:37:20,497 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:37:20,808 628 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:37:20,950 770 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (142ms total) [0 unknowns]\n2025-12-09 02:37:20,982 802 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:37:21,350 1170 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:37:21,565 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:37:21,575 1395 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:37:21,575 1395 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:37:21,575 1395 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:37:21,575 1395 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:37:21,575 1395 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:37:21,575 1395 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:37:21,909 1729 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:37:21,922 1742 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:37:21,925 1745 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:37:22,062 1882 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:37:22,072 1892 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:37:22,082 1902 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:22,092 1912 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:22,097 1917 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:37:22,106 1926 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:22,115 1935 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:22,140 1960 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:37:22,181 2001 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4740\n2025-12-09 02:37:22,190 2010 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:22,193 2013 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:22,193 2013 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.528\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:37:16,106 INFO [ omero.gateway] (MainThread) created connection (uuid=4c045218-b205-46e0-974f-41dca00f9bd4) I2025-12-09 02:37:16,164 INFO [ omero.gateway] (MainThread) created connection (uuid=a9f28902-fe5e-45f1-a10c-a7ef3f9db1c8) 2025-12-09 02:37:22,346 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=4c045218-b205-46e0-974f-41dca00f9bd4) INFO omero.gateway:__init__.py:2307 created connection (uuid=a9f28902-fe5e-45f1-a10c-a7ef3f9db1c8) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ______________ ERROR at setup of TestImage.testExposureTimeUnits _______________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 00c32f6d-bf3c-4dc7-ac61-4e315f307902 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:37:26,889 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:37:26,904 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:37:26,952 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:37:26,953 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:37:27,256 608 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:37:27,393 745 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 135ms. (137ms total) [0 unknowns]\n2025-12-09 02:37:27,424 776 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:37:27,797 1149 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:37:28,021 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:37:28,025 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:37:28,025 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:37:28,025 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:37:28,025 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:37:28,025 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:37:28,025 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:37:28,361 1713 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:37:28,374 1726 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:37:28,377 1729 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:37:28,516 1868 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:37:28,526 1878 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:37:28,536 1888 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:28,545 1897 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:28,551 1903 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:37:28,560 1912 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:28,568 1920 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:28,594 1946 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:37:28,633 1985 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4744\n2025-12-09 02:37:28,642 1994 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:28,644 1996 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:28,644 1996 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.522\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:37:22,427 INFO [ omero.gateway] (MainThread) created connection (uuid=8695044c-2135-48f2-9523-9a7be6ad9e3b) I2025-12-09 02:37:22,485 INFO [ omero.gateway] (MainThread) created connection (uuid=00c32f6d-bf3c-4dc7-ac61-4e315f307902) 2025-12-09 02:37:28,786 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=8695044c-2135-48f2-9523-9a7be6ad9e3b) INFO omero.gateway:__init__.py:2307 created connection (uuid=00c32f6d-bf3c-4dc7-ac61-4e315f307902) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) __________________ ERROR at setup of TestImage.testShortname ___________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 78fbdb7b-69b8-4e6d-b1a0-4ef324973537 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:37:33,323 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:37:33,338 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:37:33,386 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:37:33,387 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:37:33,690 608 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:37:33,826 744 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (136ms total) [0 unknowns]\n2025-12-09 02:37:33,857 775 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:37:34,211 1129 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:37:34,406 1324 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:37:34,416 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:37:34,416 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:37:34,416 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:37:34,416 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:37:34,416 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:37:34,416 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:37:34,746 1664 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:37:34,759 1677 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:37:34,762 1680 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:37:34,903 1821 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:37:34,913 1831 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:37:34,924 1842 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:34,933 1851 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:34,938 1856 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:37:34,947 1865 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:34,958 1876 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:34,983 1901 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:37:35,022 1940 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4748\n2025-12-09 02:37:35,032 1950 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:35,035 1953 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:35,035 1953 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.529\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:37:28,873 INFO [ omero.gateway] (MainThread) created connection (uuid=a82beaee-cc58-488a-973c-89a33f8787c8) I2025-12-09 02:37:28,935 INFO [ omero.gateway] (MainThread) created connection (uuid=78fbdb7b-69b8-4e6d-b1a0-4ef324973537) 2025-12-09 02:37:35,177 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=a82beaee-cc58-488a-973c-89a33f8787c8) INFO omero.gateway:__init__.py:2307 created connection (uuid=78fbdb7b-69b8-4e6d-b1a0-4ef324973537) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) __________________ ERROR at setup of TestImage.testImageDate ___________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k f398bd73-a7d8-41f5-be17-48af9c98b19a -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:37:39,130 248 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:37:39,145 263 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:37:39,194 312 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:37:39,195 313 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:37:39,497 615 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:37:39,633 751 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (136ms total) [0 unknowns]\n2025-12-09 02:37:39,664 782 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:37:40,019 1137 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:37:40,213 1331 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:37:40,218 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:37:40,218 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:37:40,218 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:37:40,218 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:37:40,218 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:37:40,218 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:37:40,554 1672 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:37:40,566 1684 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:37:40,570 1688 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:37:40,714 1832 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:37:40,724 1842 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:37:40,734 1852 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:40,744 1862 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:40,749 1867 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:37:40,758 1876 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:40,767 1885 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:40,793 1911 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:37:40,832 1950 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4752\n2025-12-09 02:37:40,841 1959 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:40,844 1962 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:40,844 1962 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.530\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:37:35,259 INFO [ omero.gateway] (MainThread) created connection (uuid=c5007b09-9543-43df-a08b-95176a34d9b0) I2025-12-09 02:37:35,317 INFO [ omero.gateway] (MainThread) created connection (uuid=f398bd73-a7d8-41f5-be17-48af9c98b19a) 2025-12-09 02:37:41,000 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=c5007b09-9543-43df-a08b-95176a34d9b0) INFO omero.gateway:__init__.py:2307 created connection (uuid=f398bd73-a7d8-41f5-be17-48af9c98b19a) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ________________ ERROR at setup of TestImage.testSimpleMarshal _________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 627ca3e9-7501-465f-b85a-ed16869cf6e1 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:37:45,659 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:37:45,674 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:37:45,721 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:37:45,722 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:37:46,022 605 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:37:46,159 742 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (136ms total) [0 unknowns]\n2025-12-09 02:37:46,189 772 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:37:46,539 1122 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:37:46,732 1315 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:37:46,737 1320 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:37:46,737 1320 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:37:46,737 1320 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:37:46,737 1320 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:37:46,737 1320 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:37:46,737 1320 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:37:47,069 1652 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:37:47,082 1665 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:37:47,085 1668 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:37:47,221 1804 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:37:47,231 1814 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:37:47,241 1824 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:47,250 1833 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:47,255 1838 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:37:47,264 1847 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:47,273 1856 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:47,298 1881 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:37:47,337 1920 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4756\n2025-12-09 02:37:47,348 1931 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:47,350 1933 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:47,350 1933 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.519\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:37:41,079 INFO [ omero.gateway] (MainThread) created connection (uuid=ca374814-ce91-4186-99f5-a14f5c3f5d39) I2025-12-09 02:37:41,136 INFO [ omero.gateway] (MainThread) created connection (uuid=627ca3e9-7501-465f-b85a-ed16869cf6e1) 2025-12-09 02:37:47,503 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=ca374814-ce91-4186-99f5-a14f5c3f5d39) INFO omero.gateway:__init__.py:2307 created connection (uuid=627ca3e9-7501-465f-b85a-ed16869cf6e1) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ____________________ ERROR at setup of TestImage.testExport ____________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 5d24e316-fea0-48aa-8310-275f907c905a -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:37:51,866 254 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:37:51,882 270 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:37:51,931 319 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:37:51,932 320 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:37:52,250 638 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:37:52,399 787 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 145ms. (149ms total) [0 unknowns]\n2025-12-09 02:37:52,431 819 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:37:52,805 1193 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:37:53,011 1399 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:37:53,015 1403 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:37:53,015 1403 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:37:53,015 1403 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:37:53,015 1403 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:37:53,015 1403 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:37:53,015 1403 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:37:53,360 1748 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:37:53,371 1759 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:37:53,374 1762 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:37:53,511 1899 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:37:53,521 1909 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:37:53,531 1919 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:53,540 1928 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:53,546 1934 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:37:53,555 1943 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:53,564 1952 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:53,588 1976 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:37:53,629 2017 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4760\n2025-12-09 02:37:53,637 2025 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:53,640 2028 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:53,640 2028 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.528\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:37:47,587 INFO [ omero.gateway] (MainThread) created connection (uuid=ac37b93d-c982-48f7-a5b8-7c72719aa034) I2025-12-09 02:37:47,647 INFO [ omero.gateway] (MainThread) created connection (uuid=5d24e316-fea0-48aa-8310-275f907c905a) 2025-12-09 02:37:53,796 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=ac37b93d-c982-48f7-a5b8-7c72719aa034) INFO omero.gateway:__init__.py:2307 created connection (uuid=5d24e316-fea0-48aa-8310-275f907c905a) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _______________ ERROR at setup of TestImage.testRenderJpegRegion _______________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 61b3285b-09fc-4de8-b70d-74f490c3ee44 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:37:58,207 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:37:58,222 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:37:58,270 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:37:58,271 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:37:58,573 607 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:37:58,715 749 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (142ms total) [0 unknowns]\n2025-12-09 02:37:58,747 781 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:37:59,112 1146 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:37:59,311 1345 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:37:59,315 1349 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:37:59,316 1350 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:37:59,316 1350 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:37:59,316 1350 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:37:59,316 1350 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:37:59,316 1350 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:37:59,648 1682 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:37:59,661 1695 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:37:59,664 1698 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:37:59,800 1834 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:37:59,810 1844 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:37:59,837 1871 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:59,847 1881 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:37:59,852 1886 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:37:59,861 1895 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:59,871 1905 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:37:59,897 1931 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:37:59,933 1967 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4764\n2025-12-09 02:37:59,946 1980 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:59,949 1983 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:37:59,949 1983 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.539\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:37:53,879 INFO [ omero.gateway] (MainThread) created connection (uuid=b49a1695-b904-4ba9-9304-7d4d872e3c56) I2025-12-09 02:37:53,938 INFO [ omero.gateway] (MainThread) created connection (uuid=61b3285b-09fc-4de8-b70d-74f490c3ee44) 2025-12-09 02:38:00,110 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=b49a1695-b904-4ba9-9304-7d4d872e3c56) INFO omero.gateway:__init__.py:2307 created connection (uuid=61b3285b-09fc-4de8-b70d-74f490c3ee44) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _________ ERROR at setup of TestImage.testRenderJpegRegion_resolution __________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k db6701a9-e412-4072-a259-e5426e782389 -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:38:04,822 248 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:38:04,837 263 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:38:04,886 312 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:38:04,887 313 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:38:05,195 621 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:38:05,334 760 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (139ms total) [0 unknowns]\n2025-12-09 02:38:05,365 791 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:38:05,727 1153 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:38:05,929 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:38:05,934 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:38:05,934 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:38:05,934 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:38:05,934 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:38:05,934 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:38:05,934 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:38:06,272 1698 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:38:06,284 1710 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:38:06,287 1713 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:38:06,425 1851 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:38:06,435 1861 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:38:06,445 1871 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:38:06,454 1880 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:38:06,459 1885 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:38:06,468 1894 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:38:06,477 1903 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:38:06,502 1928 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:38:06,541 1967 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4768\n2025-12-09 02:38:06,553 1979 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:38:06,555 1981 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:38:06,555 1981 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.523\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:38:00,191 INFO [ omero.gateway] (MainThread) created connection (uuid=ead930d9-e32c-4df7-9871-127dd6dbb799) I2025-12-09 02:38:00,248 INFO [ omero.gateway] (MainThread) created connection (uuid=db6701a9-e412-4072-a259-e5426e782389) 2025-12-09 02:38:06,715 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=ead930d9-e32c-4df7-9871-127dd6dbb799) INFO omero.gateway:__init__.py:2307 created connection (uuid=db6701a9-e412-4072-a259-e5426e782389) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _____ ERROR at setup of TestImage.testRenderJpegRegion_invalid_resolution ______ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 7e139d7a-835a-4fb7-84eb-485e70e7ecbc -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:38:10,592 244 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:38:10,607 259 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:38:10,656 308 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:38:10,657 309 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:38:10,964 616 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:38:11,105 757 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 139ms. (141ms total) [0 unknowns]\n2025-12-09 02:38:11,137 789 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:38:11,503 1155 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:38:11,700 1352 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:38:11,704 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:38:11,704 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:38:11,704 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:38:11,704 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:38:11,704 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:38:11,704 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:38:12,035 1687 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:38:12,047 1699 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:38:12,050 1702 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:38:12,186 1838 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:38:12,196 1848 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:38:12,206 1858 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:38:12,215 1867 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:38:12,219 1871 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:38:12,229 1881 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:38:12,237 1889 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:38:12,262 1914 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:38:12,302 1954 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4772\n2025-12-09 02:38:12,313 1965 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:38:12,316 1968 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:38:12,316 1968 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.518\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:38:06,796 INFO [ omero.gateway] (MainThread) created connection (uuid=bb711b65-87e6-4ba7-9dad-676bfb6f69b8) I2025-12-09 02:38:06,854 INFO [ omero.gateway] (MainThread) created connection (uuid=7e139d7a-835a-4fb7-84eb-485e70e7ecbc) 2025-12-09 02:38:12,469 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=bb711b65-87e6-4ba7-9dad-676bfb6f69b8) INFO omero.gateway:__init__.py:2307 created connection (uuid=7e139d7a-835a-4fb7-84eb-485e70e7ecbc) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ______________ ERROR at setup of TestImage.testRenderBirdsEyeView ______________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k d4cf942e-3c49-450f-9fcb-6c1243f57f7f -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:38:17,288 255 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:38:17,303 270 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:38:17,353 320 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:38:17,354 321 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:38:17,667 634 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:38:17,808 775 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 139ms. (142ms total) [0 unknowns]\n2025-12-09 02:38:17,840 807 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:38:18,208 1175 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:38:18,421 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:38:18,425 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:38:18,425 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:38:18,425 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:38:18,426 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:38:18,426 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:38:18,426 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:38:18,774 1741 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:38:18,787 1754 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:38:18,790 1757 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:38:19,003 1970 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:38:19,012 1979 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:38:19,023 1990 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:38:19,031 1998 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:38:19,036 2003 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:38:19,045 2012 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:38:19,053 2020 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:38:19,083 2050 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:38:19,126 2093 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4776\n2025-12-09 02:38:19,138 2105 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:38:19,141 2108 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:38:19,141 2108 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.615\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:38:12,551 INFO [ omero.gateway] (MainThread) created connection (uuid=da74ebd1-d129-4547-b9ac-75e4d665ee62) I2025-12-09 02:38:12,609 INFO [ omero.gateway] (MainThread) created connection (uuid=d4cf942e-3c49-450f-9fcb-6c1243f57f7f) 2025-12-09 02:38:19,288 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=da74ebd1-d129-4547-b9ac-75e4d665ee62) INFO omero.gateway:__init__.py:2307 created connection (uuid=d4cf942e-3c49-450f-9fcb-6c1243f57f7f) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ___________ ERROR at setup of TestImage.testRenderBirdsEyeView_Size ____________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k aea1a7ab-9c95-4856-83b1-5d09a137054f -p 14064 import -d 1059 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:38:23,779 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:38:23,794 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:38:23,843 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:38:23,844 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:38:24,153 626 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:38:24,293 766 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (140ms total) [0 unknowns]\n2025-12-09 02:38:24,325 798 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:38:24,688 1161 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:38:24,888 1361 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:38:24,897 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:38:24,898 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:38:24,898 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:38:24,898 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:38:24,898 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:38:24,898 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:38:25,238 1711 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1059\n2025-12-09 02:38:25,251 1724 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1059\n2025-12-09 02:38:25,254 1727 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:38:25,400 1873 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:38:25,410 1883 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:38:25,421 1894 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:38:25,430 1903 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:38:25,435 1908 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:38:25,445 1918 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:38:25,454 1927 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:38:25,481 1954 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:38:25,518 1991 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4780\n2025-12-09 02:38:25,544 2017 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:38:25,547 2020 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:38:25,548 2021 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.556\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:38:19,376 INFO [ omero.gateway] (MainThread) created connection (uuid=dfd4b1e5-9574-42f3-84af-434d13ddf018) I2025-12-09 02:38:19,436 INFO [ omero.gateway] (MainThread) created connection (uuid=aea1a7ab-9c95-4856-83b1-5d09a137054f) 2025-12-09 02:38:25,692 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=dfd4b1e5-9574-42f3-84af-434d13ddf018) INFO omero.gateway:__init__.py:2307 created connection (uuid=aea1a7ab-9c95-4856-83b1-5d09a137054f) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _____________ ERROR at setup of TestPixels.testReuseRawPixelsStore _____________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k d6382fee-f997-40c0-91d5-75ed121ad27f -p 14064 import -d 1068 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:38:47,613 244 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:38:47,628 259 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:38:47,676 307 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:38:47,677 308 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:38:47,984 615 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:38:48,122 753 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (139ms total) [0 unknowns]\n2025-12-09 02:38:48,153 784 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:38:48,509 1140 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:38:48,704 1335 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:38:48,708 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:38:48,709 1340 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:38:48,709 1340 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:38:48,709 1340 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:38:48,709 1340 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:38:48,709 1340 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:38:49,053 1684 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1068\n2025-12-09 02:38:49,066 1697 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1068\n2025-12-09 02:38:49,069 1700 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:38:49,235 1866 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:38:49,245 1876 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:38:49,258 1889 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:38:49,267 1898 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:38:49,273 1904 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:38:49,283 1914 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:38:49,292 1923 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:38:49,325 1956 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:38:49,364 1995 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4784\n2025-12-09 02:38:49,372 2003 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:38:49,375 2006 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:38:49,375 2006 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.570\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:38:41,874 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:38:41,879 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:38:41,916 INFO [ omero.gateway] (MainThread) created connection (uuid=c575961e-6033-4284-b2ab-7731bfc49ba2) 2025-12-09 02:38:42,339 INFO [ omero.gateway] (MainThread) created connection (uuid=8355865c-aec7-4b88-9faf-d434dfa3088c) 2025-12-09 02:38:42,374 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:38:42,409 INFO [ omero.gateway] (MainThread) created connection (uuid=6c6a5308-fd7f-4359-89be-0402c479ac7d) 2025-12-09 02:38:42,442 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:38:42,474 INFO [ omero.gateway] (MainThread) created connection (uuid=a9e006a6-4330-44c8-8214-b5317def2e39) 2025-12-09 02:38:42,513 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:38:42,548 INFO [ omero.gateway] (MainThread) created connection (uuid=2c123d1d-f981-4b72-b960-cb7225df2e9a) 2025-12-09 02:38:42,585 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:38:42,619 INFO [ omero.gateway] (MainThread) created connection (uuid=041a6ad9-6c25-4dd6-aa17-161bddc8da84) 2025-12-09 02:38:42,655 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:38:42,690 INFO [ omero.gateway] (MainThread) created connection (uuid=25aa1114-51fe-443b-9ec1-f3a83520d073) 2025-12-09 02:38:42,727 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:38:42,760 INFO [ omero.gateway] (MainThread) created connection (uuid=3f7f4275-ece4-4321-9ef7-a6c0b5396630) 2025-12-09 02:38:42,805 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:38:42,839 INFO [ omero.gateway] (MainThread) created connection (uuid=fd8ff0f2-9cea-449a-97df-19b64f825f80) 2025-12-09 02:38:42,885 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:38:42,919 INFO [ omero.gateway] (MainThread) created connection (uuid=98078add-5b2f-4b1e-9035-f98f1270b190) 2025-12-09 02:38:42,961 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:38:42,965 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:38:42,999 INFO [ omero.gateway] (MainThread) created connection (uuid=81087d64-1ef0-4067-9cee-352724d4e30d) 2025-12-09 02:38:43,064 INFO [ omero.gateway] (MainThread) created connection (uuid=b6e25c21-abee-4cf9-900f-4d0eb54c2313) I2025-12-09 02:38:43,125 INFO [ omero.gateway] (MainThread) created connection (uuid=d6382fee-f997-40c0-91d5-75ed121ad27f) 2025-12-09 02:38:49,529 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=c575961e-6033-4284-b2ab-7731bfc49ba2) INFO omero.gateway:__init__.py:2307 created connection (uuid=8355865c-aec7-4b88-9faf-d434dfa3088c) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=6c6a5308-fd7f-4359-89be-0402c479ac7d) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=a9e006a6-4330-44c8-8214-b5317def2e39) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=2c123d1d-f981-4b72-b960-cb7225df2e9a) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=041a6ad9-6c25-4dd6-aa17-161bddc8da84) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=25aa1114-51fe-443b-9ec1-f3a83520d073) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=3f7f4275-ece4-4321-9ef7-a6c0b5396630) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=fd8ff0f2-9cea-449a-97df-19b64f825f80) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=98078add-5b2f-4b1e-9035-f98f1270b190) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=81087d64-1ef0-4067-9cee-352724d4e30d) INFO omero.gateway:__init__.py:2307 created connection (uuid=b6e25c21-abee-4cf9-900f-4d0eb54c2313) INFO omero.gateway:__init__.py:2307 created connection (uuid=d6382fee-f997-40c0-91d5-75ed121ad27f) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) __________________ ERROR at setup of TestPixels.testPlaneInfo __________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 6f7e3465-30c2-4b81-a78e-59da50e5a57e -p 14064 import -d 1068 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:38:54,023 251 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:38:54,038 266 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:38:54,087 315 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:38:54,088 316 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:38:54,398 626 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:38:54,539 767 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (141ms total) [0 unknowns]\n2025-12-09 02:38:54,571 799 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:38:54,929 1157 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:38:55,155 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:38:55,160 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:38:55,160 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:38:55,160 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:38:55,160 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:38:55,160 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:38:55,160 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:38:55,506 1734 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1068\n2025-12-09 02:38:55,519 1747 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1068\n2025-12-09 02:38:55,522 1750 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:38:55,674 1902 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:38:55,684 1912 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:38:55,694 1922 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:38:55,703 1931 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:38:55,708 1936 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:38:55,717 1945 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:38:55,727 1955 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:38:55,752 1980 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:38:55,791 2019 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4788\n2025-12-09 02:38:55,799 2027 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:38:55,801 2029 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:38:55,801 2029 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.542\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:38:49,613 INFO [ omero.gateway] (MainThread) created connection (uuid=7937a4df-2140-46aa-8714-3d9ae136d375) I2025-12-09 02:38:49,672 INFO [ omero.gateway] (MainThread) created connection (uuid=6f7e3465-30c2-4b81-a78e-59da50e5a57e) 2025-12-09 02:38:55,955 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=7937a4df-2140-46aa-8714-3d9ae136d375) INFO omero.gateway:__init__.py:2307 created connection (uuid=6f7e3465-30c2-4b81-a78e-59da50e5a57e) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _________________ ERROR at setup of TestPixels.testPixelsType __________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k def17abe-6600-40ed-b691-3411ba2c7012 -p 14064 import -d 1068 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:39:00,371 238 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:39:00,386 253 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:39:00,434 301 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:39:00,435 302 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:39:00,733 600 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:39:00,869 736 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 133ms. (136ms total) [0 unknowns]\n2025-12-09 02:39:00,900 767 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:39:01,263 1130 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:39:01,464 1331 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:39:01,468 1335 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:39:01,468 1335 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:39:01,468 1335 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:39:01,468 1335 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:39:01,468 1335 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:39:01,468 1335 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:39:01,805 1672 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1068\n2025-12-09 02:39:01,818 1685 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1068\n2025-12-09 02:39:01,821 1688 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:39:01,969 1836 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:39:01,979 1846 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:39:01,989 1856 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:01,998 1865 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:02,004 1871 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:39:02,013 1880 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:02,022 1889 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:02,048 1915 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:39:02,086 1953 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4792\n2025-12-09 02:39:02,100 1967 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:02,103 1970 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:02,103 1970 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.541\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:38:56,041 INFO [ omero.gateway] (MainThread) created connection (uuid=68d67c1b-c00e-49c6-ada8-1657dfd087b4) I2025-12-09 02:38:56,101 INFO [ omero.gateway] (MainThread) created connection (uuid=def17abe-6600-40ed-b691-3411ba2c7012) 2025-12-09 02:39:02,246 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=68d67c1b-c00e-49c6-ada8-1657dfd087b4) INFO omero.gateway:__init__.py:2307 created connection (uuid=def17abe-6600-40ed-b691-3411ba2c7012) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ___________________ ERROR at setup of TestPixels.testGetTile ___________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 383992be-261d-41d8-82ad-753d4d51c8b9 -p 14064 import -d 1068 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:39:06,948 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:39:06,963 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:39:07,012 317 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:39:07,014 319 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:39:07,320 625 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:39:07,457 762 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 135ms. (137ms total) [0 unknowns]\n2025-12-09 02:39:07,488 793 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:39:07,846 1151 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:39:08,100 1405 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:39:08,104 1409 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:39:08,105 1410 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:39:08,105 1410 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:39:08,105 1410 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:39:08,105 1410 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:39:08,105 1410 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:39:08,452 1757 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1068\n2025-12-09 02:39:08,466 1771 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1068\n2025-12-09 02:39:08,469 1774 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:39:08,647 1952 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:39:08,657 1962 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:39:08,670 1975 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:08,679 1984 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:08,684 1989 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:39:08,695 2000 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:08,704 2009 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:08,740 2045 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:39:08,778 2083 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4796\n2025-12-09 02:39:08,796 2101 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:08,798 2103 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:08,799 2104 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.592\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:39:02,340 INFO [ omero.gateway] (MainThread) created connection (uuid=30b9661c-1a32-442a-9f81-5e01cbbf84ed) I2025-12-09 02:39:02,404 INFO [ omero.gateway] (MainThread) created connection (uuid=383992be-261d-41d8-82ad-753d4d51c8b9) 2025-12-09 02:39:08,946 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=30b9661c-1a32-442a-9f81-5e01cbbf84ed) INFO omero.gateway:__init__.py:2307 created connection (uuid=383992be-261d-41d8-82ad-753d4d51c8b9) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) __________________ ERROR at setup of TestPixels.testGetPlane ___________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 09aa491e-0577-4931-a3cc-5fab0ff10359 -p 14064 import -d 1068 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:39:12,979 254 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:39:12,994 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:39:13,043 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:39:13,044 319 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:39:13,354 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:39:13,495 770 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (141ms total) [0 unknowns]\n2025-12-09 02:39:13,527 802 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:39:13,891 1166 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:39:14,098 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:39:14,104 1379 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:39:14,104 1379 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:39:14,104 1379 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:39:14,104 1379 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:39:14,104 1379 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:39:14,104 1379 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:39:14,438 1713 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1068\n2025-12-09 02:39:14,451 1726 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1068\n2025-12-09 02:39:14,454 1729 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:39:14,596 1871 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:39:14,606 1881 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:39:14,617 1892 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:14,627 1902 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:14,631 1906 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:39:14,642 1917 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:14,650 1925 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:14,678 1953 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:39:14,717 1992 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4800\n2025-12-09 02:39:14,726 2001 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:14,729 2004 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:14,729 2004 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.532\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:39:09,036 INFO [ omero.gateway] (MainThread) created connection (uuid=d4bb03a6-55bc-4bee-ad98-af2504bd5f43) I2025-12-09 02:39:09,100 INFO [ omero.gateway] (MainThread) created connection (uuid=09aa491e-0577-4931-a3cc-5fab0ff10359) 2025-12-09 02:39:14,878 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=d4bb03a6-55bc-4bee-ad98-af2504bd5f43) INFO omero.gateway:__init__.py:2307 created connection (uuid=09aa491e-0577-4931-a3cc-5fab0ff10359) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ________ ERROR at setup of TestPixels.testGetPlanesExceptionOnGetPlane _________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 56ccf75b-79d2-4f6f-bea1-d65e63e4423b -p 14064 import -d 1068 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:39:19,560 255 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:39:19,575 270 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:39:19,625 320 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:39:19,626 321 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:39:19,939 634 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:39:20,078 773 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (139ms total) [0 unknowns]\n2025-12-09 02:39:20,110 805 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:39:20,473 1168 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:39:20,672 1367 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:39:20,678 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:39:20,678 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:39:20,678 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:39:20,678 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:39:20,678 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:39:20,678 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:39:21,025 1720 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1068\n2025-12-09 02:39:21,039 1734 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1068\n2025-12-09 02:39:21,042 1737 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:39:21,188 1883 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:39:21,197 1892 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:39:21,208 1903 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:21,218 1913 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:21,223 1918 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:39:21,232 1927 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:21,242 1937 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:21,268 1963 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:39:21,306 2001 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4804\n2025-12-09 02:39:21,314 2009 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:21,317 2012 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:21,317 2012 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.542\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:39:14,965 INFO [ omero.gateway] (MainThread) created connection (uuid=00e2bbfe-8654-4810-872d-02a3d859287a) I2025-12-09 02:39:15,030 INFO [ omero.gateway] (MainThread) created connection (uuid=56ccf75b-79d2-4f6f-bea1-d65e63e4423b) 2025-12-09 02:39:21,464 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=00e2bbfe-8654-4810-872d-02a3d859287a) INFO omero.gateway:__init__.py:2307 created connection (uuid=56ccf75b-79d2-4f6f-bea1-d65e63e4423b) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) __________ ERROR at setup of TestPixels.testGetPlanesExceptionOnClose __________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k e3c4bc48-969c-48e8-a078-573802e7b30f -p 14064 import -d 1068 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:39:25,902 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:39:25,917 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:39:25,964 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:39:25,965 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:39:26,264 604 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:39:26,401 741 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (137ms total) [0 unknowns]\n2025-12-09 02:39:26,432 772 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:39:26,798 1138 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:39:27,006 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:39:27,010 1350 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:39:27,010 1350 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:39:27,010 1350 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:39:27,010 1350 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:39:27,010 1350 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:39:27,010 1350 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:39:27,346 1686 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1068\n2025-12-09 02:39:27,359 1699 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1068\n2025-12-09 02:39:27,362 1702 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:39:27,512 1852 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:39:27,521 1861 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:39:27,532 1872 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:27,540 1880 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:27,546 1886 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:39:27,556 1896 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:27,565 1905 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:27,589 1929 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:39:27,626 1966 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4808\n2025-12-09 02:39:27,636 1976 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:27,639 1979 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:27,639 1979 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.531\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:39:21,549 INFO [ omero.gateway] (MainThread) created connection (uuid=92ccfbf1-ad9e-4496-96e7-d1d85666a041) I2025-12-09 02:39:21,612 INFO [ omero.gateway] (MainThread) created connection (uuid=e3c4bc48-969c-48e8-a078-573802e7b30f) 2025-12-09 02:39:27,780 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=92ccfbf1-ad9e-4496-96e7-d1d85666a041) INFO omero.gateway:__init__.py:2307 created connection (uuid=e3c4bc48-969c-48e8-a078-573802e7b30f) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) __________ ERROR at setup of TestPixels.testGetPlanesExceptionOnBoth ___________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k cba7968d-6686-4ad1-819a-558819ff8ee8 -p 14064 import -d 1068 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:39:32,202 240 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:39:32,217 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:39:32,264 302 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:39:32,265 303 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:39:32,567 605 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:39:32,704 742 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (137ms total) [0 unknowns]\n2025-12-09 02:39:32,734 772 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:39:33,088 1126 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:39:33,281 1319 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:39:33,284 1322 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:39:33,285 1323 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:39:33,285 1323 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:39:33,285 1323 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:39:33,285 1323 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:39:33,285 1323 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:39:33,620 1658 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1068\n2025-12-09 02:39:33,633 1671 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1068\n2025-12-09 02:39:33,636 1674 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:39:33,779 1817 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:39:33,788 1826 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:39:33,799 1837 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:33,808 1846 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:33,813 1851 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:39:33,822 1860 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:33,832 1870 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:33,857 1895 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:39:33,896 1934 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4812\n2025-12-09 02:39:33,905 1943 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:33,908 1946 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:33,908 1946 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.528\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:39:27,865 INFO [ omero.gateway] (MainThread) created connection (uuid=634549c7-77b6-4799-8447-32e9ad148fca) I2025-12-09 02:39:27,924 INFO [ omero.gateway] (MainThread) created connection (uuid=cba7968d-6686-4ad1-819a-558819ff8ee8) 2025-12-09 02:39:34,050 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=634549c7-77b6-4799-8447-32e9ad148fca) INFO omero.gateway:__init__.py:2307 created connection (uuid=cba7968d-6686-4ad1-819a-558819ff8ee8) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ________________ ERROR at setup of TestPixels.testGetHistogram _________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k d6467136-8340-4b3f-a5d1-c208ebe35347 -p 14064 import -d 1068 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:39:38,563 243 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:39:38,578 258 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:39:38,625 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:39:38,626 306 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:39:38,930 610 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:39:39,068 748 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (138ms total) [0 unknowns]\n2025-12-09 02:39:39,099 779 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:39:39,453 1133 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:39:39,651 1331 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:39:39,654 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:39:39,655 1335 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:39:39,655 1335 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:39:39,655 1335 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:39:39,655 1335 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:39:39,655 1335 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:39:39,991 1671 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1068\n2025-12-09 02:39:40,003 1683 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1068\n2025-12-09 02:39:40,006 1686 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:39:40,143 1823 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:39:40,153 1833 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:39:40,163 1843 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:40,172 1852 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:40,177 1857 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:39:40,186 1866 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:40,195 1875 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:40,220 1900 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:39:40,260 1940 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4816\n2025-12-09 02:39:40,270 1950 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:40,273 1953 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:40,273 1953 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.521\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:39:34,133 INFO [ omero.gateway] (MainThread) created connection (uuid=589420f0-c44e-4b5d-9d79-8deda63b950f) I2025-12-09 02:39:34,193 INFO [ omero.gateway] (MainThread) created connection (uuid=d6467136-8340-4b3f-a5d1-c208ebe35347) 2025-12-09 02:39:40,430 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=589420f0-c44e-4b5d-9d79-8deda63b950f) INFO omero.gateway:__init__.py:2307 created connection (uuid=d6467136-8340-4b3f-a5d1-c208ebe35347) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ___________________ ERROR at setup of TestRDefs.testDefault ____________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 4650ba87-6533-4413-a11a-44bcc9c930a5 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:39:48,101 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:39:48,116 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:39:48,165 314 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:39:48,166 315 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:39:48,476 625 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:39:48,618 767 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (142ms total) [0 unknowns]\n2025-12-09 02:39:48,650 799 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:39:49,014 1163 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:39:49,229 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:39:49,238 1387 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:39:49,238 1387 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:39:49,238 1387 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:39:49,238 1387 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:39:49,238 1387 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:39:49,238 1387 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:39:49,583 1732 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:39:49,597 1746 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:39:49,600 1749 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:39:49,741 1890 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:39:49,750 1899 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:39:49,760 1909 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:49,769 1918 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:49,774 1923 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:39:49,784 1933 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:49,793 1942 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:49,818 1967 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:39:49,857 2006 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4820\n2025-12-09 02:39:49,867 2016 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:49,870 2019 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:49,870 2019 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.539\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:39:43,111 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:39:43,116 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:39:43,150 INFO [ omero.gateway] (MainThread) created connection (uuid=e5eabcca-99b4-4083-afff-10ce90fd43b0) 2025-12-09 02:39:43,568 INFO [ omero.gateway] (MainThread) created connection (uuid=ccd833e2-9b7e-4ba4-9b2c-362db55869c4) 2025-12-09 02:39:43,601 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:39:43,635 INFO [ omero.gateway] (MainThread) created connection (uuid=0cb0dee6-7ef7-4285-8269-7c927e9fad5b) 2025-12-09 02:39:43,668 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:39:43,702 INFO [ omero.gateway] (MainThread) created connection (uuid=78b265f2-9dc2-431d-a09b-658a88ed810f) 2025-12-09 02:39:43,738 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:39:43,771 INFO [ omero.gateway] (MainThread) created connection (uuid=46632a8e-2803-496b-916b-4a199902dfea) 2025-12-09 02:39:43,807 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:39:43,840 INFO [ omero.gateway] (MainThread) created connection (uuid=af4816f6-d2dd-4ec9-b064-c2de6443c9b1) 2025-12-09 02:39:43,878 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:39:43,911 INFO [ omero.gateway] (MainThread) created connection (uuid=c63544e3-9561-4fb8-9694-de9d1aaefd43) 2025-12-09 02:39:43,946 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:39:43,979 INFO [ omero.gateway] (MainThread) created connection (uuid=a9a4c5f0-3649-4781-be28-2092d5802bc8) 2025-12-09 02:39:44,021 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:39:44,055 INFO [ omero.gateway] (MainThread) created connection (uuid=80a92ffd-e056-4021-bd2b-eb3f7a9d183e) 2025-12-09 02:39:44,098 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:39:44,131 INFO [ omero.gateway] (MainThread) created connection (uuid=d7f5aa16-a309-4d63-a1b5-1bb8ae2d529e) 2025-12-09 02:39:44,172 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:39:44,175 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:39:44,210 INFO [ omero.gateway] (MainThread) created connection (uuid=126ba8da-f1a6-436a-aee4-3056fbb9f267) 2025-12-09 02:39:44,273 INFO [ omero.gateway] (MainThread) created connection (uuid=6c1a3650-9b06-4f97-8278-3268297f49f0) I2025-12-09 02:39:44,332 INFO [ omero.gateway] (MainThread) created connection (uuid=4650ba87-6533-4413-a11a-44bcc9c930a5) 2025-12-09 02:39:50,019 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=e5eabcca-99b4-4083-afff-10ce90fd43b0) INFO omero.gateway:__init__.py:2307 created connection (uuid=ccd833e2-9b7e-4ba4-9b2c-362db55869c4) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=0cb0dee6-7ef7-4285-8269-7c927e9fad5b) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=78b265f2-9dc2-431d-a09b-658a88ed810f) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=46632a8e-2803-496b-916b-4a199902dfea) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=af4816f6-d2dd-4ec9-b064-c2de6443c9b1) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=c63544e3-9561-4fb8-9694-de9d1aaefd43) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=a9a4c5f0-3649-4781-be28-2092d5802bc8) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=80a92ffd-e056-4021-bd2b-eb3f7a9d183e) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=d7f5aa16-a309-4d63-a1b5-1bb8ae2d529e) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=126ba8da-f1a6-436a-aee4-3056fbb9f267) INFO omero.gateway:__init__.py:2307 created connection (uuid=6c1a3650-9b06-4f97-8278-3268297f49f0) INFO omero.gateway:__init__.py:2307 created connection (uuid=4650ba87-6533-4413-a11a-44bcc9c930a5) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) __________________ ERROR at setup of TestRDefs.testCustomized __________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k a061157b-7c82-4bc7-a61b-c577c0406ef0 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:39:54,794 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:39:54,809 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:39:54,857 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:39:54,858 306 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:39:55,160 608 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:39:55,297 745 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 135ms. (137ms total) [0 unknowns]\n2025-12-09 02:39:55,328 776 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:39:55,681 1129 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:39:55,884 1332 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:39:55,888 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:39:55,888 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:39:55,888 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:39:55,888 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:39:55,888 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:39:55,888 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:39:56,223 1671 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:39:56,235 1683 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:39:56,239 1687 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:39:56,378 1826 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:39:56,388 1836 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:39:56,398 1846 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:56,409 1857 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:39:56,414 1862 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:39:56,425 1873 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:56,435 1883 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:39:56,461 1909 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:39:56,498 1946 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4824\n2025-12-09 02:39:56,511 1959 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:56,514 1962 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:39:56,515 1963 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.535\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:39:50,106 INFO [ omero.gateway] (MainThread) created connection (uuid=56a2b42c-c099-44f8-860a-6feb8eaaf310) I2025-12-09 02:39:50,170 INFO [ omero.gateway] (MainThread) created connection (uuid=a061157b-7c82-4bc7-a61b-c577c0406ef0) 2025-12-09 02:39:56,673 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=56a2b42c-c099-44f8-860a-6feb8eaaf310) INFO omero.gateway:__init__.py:2307 created connection (uuid=a061157b-7c82-4bc7-a61b-c577c0406ef0) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ________________ ERROR at setup of TestRDefs.testChannelWindows ________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k f3bd8d69-1d42-4b86-b1ae-d59d67e74610 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:40:01,250 251 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:40:01,265 266 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:40:01,314 315 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:40:01,315 316 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:40:01,625 626 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:40:01,766 767 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (141ms total) [0 unknowns]\n2025-12-09 02:40:01,798 799 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:40:02,154 1155 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:40:02,352 1353 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:40:02,356 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:40:02,356 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:40:02,356 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:40:02,356 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:40:02,356 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:40:02,356 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:40:03,406 2407 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:40:03,419 2420 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:40:03,424 2425 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:40:03,565 2566 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:40:03,574 2575 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:40:03,585 2586 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:03,594 2595 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:03,599 2600 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:40:03,608 2609 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:03,618 2619 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:03,643 2644 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:40:03,692 2693 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4828\n2025-12-09 02:40:03,697 2698 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:03,700 2701 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:03,700 2701 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.532\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:39:56,760 INFO [ omero.gateway] (MainThread) created connection (uuid=9f7859df-6949-4e49-956f-aab521bad5ad) I2025-12-09 02:39:56,822 INFO [ omero.gateway] (MainThread) created connection (uuid=f3bd8d69-1d42-4b86-b1ae-d59d67e74610) 2025-12-09 02:40:03,856 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=9f7859df-6949-4e49-956f-aab521bad5ad) INFO omero.gateway:__init__.py:2307 created connection (uuid=f3bd8d69-1d42-4b86-b1ae-d59d67e74610) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ______________ ERROR at setup of TestRDefs.testFloatDefaultMinMax ______________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k b2ddf8de-7b5f-430b-a2d1-c407b4e09534 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:40:08,482 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:40:08,497 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:40:08,546 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:40:08,547 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:40:08,855 625 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:40:08,996 766 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 139ms. (141ms total) [0 unknowns]\n2025-12-09 02:40:09,028 798 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:40:09,402 1172 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:40:09,608 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:40:09,612 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:40:09,612 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:40:09,612 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:40:09,612 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:40:09,612 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:40:09,612 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:40:09,960 1730 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:40:09,973 1743 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:40:09,976 1746 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:40:10,115 1885 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:40:10,125 1895 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:40:10,135 1905 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:10,144 1914 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:10,149 1919 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:40:10,159 1929 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:10,168 1938 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:10,193 1963 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:40:10,233 2003 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4832\n2025-12-09 02:40:10,239 2009 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:10,242 2012 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:10,242 2012 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.530\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:40:03,940 INFO [ omero.gateway] (MainThread) created connection (uuid=f5cb3059-e85f-450f-b850-696e4125d186) I2025-12-09 02:40:04,004 INFO [ omero.gateway] (MainThread) created connection (uuid=b2ddf8de-7b5f-430b-a2d1-c407b4e09534) 2025-12-09 02:40:10,400 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=f5cb3059-e85f-450f-b850-696e4125d186) INFO omero.gateway:__init__.py:2307 created connection (uuid=b2ddf8de-7b5f-430b-a2d1-c407b4e09534) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _________________ ERROR at setup of TestRDefs.testEmissionWave _________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 85c28ba3-9a37-465b-b083-2b69d3298e28 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:40:15,209 251 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:40:15,224 266 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:40:15,273 315 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:40:15,274 316 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:40:15,585 627 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:40:15,726 768 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (141ms total) [0 unknowns]\n2025-12-09 02:40:15,757 799 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:40:16,122 1164 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:40:16,322 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:40:16,325 1367 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:40:16,326 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:40:16,326 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:40:16,326 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:40:16,326 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:40:16,326 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:40:16,664 1706 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:40:16,677 1719 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:40:16,680 1722 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:40:16,823 1865 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:40:16,832 1874 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:40:16,843 1885 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:16,852 1894 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:16,857 1899 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:40:16,866 1908 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:16,876 1918 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:16,903 1945 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:40:16,943 1985 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4836\n2025-12-09 02:40:16,954 1996 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:16,956 1998 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:16,957 1999 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.534\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:40:10,484 INFO [ omero.gateway] (MainThread) created connection (uuid=a96b637d-2ddc-42b2-94e2-2e00164af33e) I2025-12-09 02:40:10,558 INFO [ omero.gateway] (MainThread) created connection (uuid=85c28ba3-9a37-465b-b083-2b69d3298e28) 2025-12-09 02:40:17,114 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=a96b637d-2ddc-42b2-94e2-2e00164af33e) INFO omero.gateway:__init__.py:2307 created connection (uuid=85c28ba3-9a37-465b-b083-2b69d3298e28) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) __________________ ERROR at setup of TestRDefs.testBatchCopy ___________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k e735dd6a-e847-427d-af6e-e7895f711f9e -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:40:21,046 238 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:40:21,061 253 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:40:21,108 300 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:40:21,109 301 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:40:21,407 599 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:40:21,543 735 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 133ms. (136ms total) [0 unknowns]\n2025-12-09 02:40:21,574 766 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:40:21,929 1121 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:40:22,130 1322 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:40:22,134 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:40:22,134 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:40:22,134 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:40:22,134 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:40:22,134 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:40:22,134 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:40:22,469 1661 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:40:22,482 1674 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:40:22,485 1677 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:40:22,621 1813 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:40:22,630 1822 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:40:22,640 1832 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:22,649 1841 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:22,654 1846 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:40:22,663 1855 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:22,672 1864 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:22,698 1890 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:40:22,735 1927 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4840\n2025-12-09 02:40:22,745 1937 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:22,748 1940 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:22,748 1940 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.526\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:40:17,196 INFO [ omero.gateway] (MainThread) created connection (uuid=e19b597f-b717-4c59-90b0-fe7a12cffbe7) I2025-12-09 02:40:17,259 INFO [ omero.gateway] (MainThread) created connection (uuid=e735dd6a-e847-427d-af6e-e7895f711f9e) 2025-12-09 02:40:22,894 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=e19b597f-b717-4c59-90b0-fe7a12cffbe7) INFO omero.gateway:__init__.py:2307 created connection (uuid=e735dd6a-e847-427d-af6e-e7895f711f9e) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ____________ ERROR at setup of TestRDefs.testGroupBasedPermissions _____________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k a825b72c-81c1-4b45-afc3-de851cc89e61 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:40:27,608 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:40:27,623 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:40:27,671 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:40:27,672 306 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:40:27,975 609 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:40:28,113 747 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (138ms total) [0 unknowns]\n2025-12-09 02:40:28,145 779 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:40:28,507 1141 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:40:28,708 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:40:28,712 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:40:28,712 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:40:28,712 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:40:28,712 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:40:28,712 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:40:28,712 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:40:29,061 1695 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:40:29,074 1708 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:40:29,077 1711 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:40:29,224 1858 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:40:29,233 1867 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:40:29,244 1878 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:29,253 1887 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:29,259 1893 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:40:29,268 1902 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:29,278 1912 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:29,305 1939 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:40:29,345 1979 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4844\n2025-12-09 02:40:29,352 1986 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:29,355 1989 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:29,355 1989 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.542\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:40:22,976 INFO [ omero.gateway] (MainThread) created connection (uuid=44435007-618c-44c9-8542-ee40788763a3) I2025-12-09 02:40:23,037 INFO [ omero.gateway] (MainThread) created connection (uuid=a825b72c-81c1-4b45-afc3-de851cc89e61) 2025-12-09 02:40:29,513 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=44435007-618c-44c9-8542-ee40788763a3) INFO omero.gateway:__init__.py:2307 created connection (uuid=a825b72c-81c1-4b45-afc3-de851cc89e61) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ___________________ ERROR at setup of TestRDefs.testGetRdefs ___________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 2adcac62-3eef-44ea-a5f8-18361fb955a9 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:40:34,030 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:40:34,045 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:40:34,092 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:40:34,093 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:40:34,393 605 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:40:34,530 742 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (137ms total) [0 unknowns]\n2025-12-09 02:40:34,561 773 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:40:34,910 1122 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:40:35,101 1313 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:40:35,105 1317 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:40:35,105 1317 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:40:35,105 1317 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:40:35,105 1317 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:40:35,105 1317 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:40:35,105 1317 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:40:35,446 1658 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:40:35,459 1671 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:40:35,462 1674 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:40:35,602 1814 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:40:35,611 1823 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:40:35,622 1834 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:35,631 1843 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:35,636 1848 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:40:35,645 1857 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:35,654 1866 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:35,680 1892 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:40:35,718 1930 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4848\n2025-12-09 02:40:35,728 1940 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:35,731 1943 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:35,731 1943 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.531\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:40:29,596 INFO [ omero.gateway] (MainThread) created connection (uuid=b79fa8d6-9ffa-49f3-ad0a-b19976a1a671) I2025-12-09 02:40:29,656 INFO [ omero.gateway] (MainThread) created connection (uuid=2adcac62-3eef-44ea-a5f8-18361fb955a9) 2025-12-09 02:40:35,885 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=b79fa8d6-9ffa-49f3-ad0a-b19976a1a671) INFO omero.gateway:__init__.py:2307 created connection (uuid=2adcac62-3eef-44ea-a5f8-18361fb955a9) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ________________ ERROR at setup of TestRDefs.testResetDefaults _________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 466c695f-6f3e-4302-8388-c4c065a48d76 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:40:40,435 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:40:40,450 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:40:40,499 317 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:40:40,500 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:40:40,811 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:40:40,951 769 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (140ms total) [0 unknowns]\n2025-12-09 02:40:40,983 801 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:40:41,346 1164 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:40:41,547 1365 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:40:41,551 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:40:41,551 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:40:41,551 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:40:41,551 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:40:41,551 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:40:41,551 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:40:41,897 1715 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:40:41,909 1727 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:40:41,913 1731 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:40:42,047 1865 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:40:42,057 1875 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:40:42,067 1885 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:42,075 1893 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:42,080 1898 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:40:42,090 1908 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:42,099 1917 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:42,124 1942 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:40:42,161 1979 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4852\n2025-12-09 02:40:42,171 1989 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:42,173 1991 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:42,174 1992 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.524\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:40:35,968 INFO [ omero.gateway] (MainThread) created connection (uuid=ff4e8b1e-032f-4e3f-a269-6be01a4adb8d) I2025-12-09 02:40:36,027 INFO [ omero.gateway] (MainThread) created connection (uuid=466c695f-6f3e-4302-8388-c4c065a48d76) 2025-12-09 02:40:42,330 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=ff4e8b1e-032f-4e3f-a269-6be01a4adb8d) INFO omero.gateway:__init__.py:2307 created connection (uuid=466c695f-6f3e-4302-8388-c4c065a48d76) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _____________ ERROR at setup of TestRDefs.testQuantizationSettings _____________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 778f6799-ad2b-48bd-a6ab-a4d2ade8ec4d -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:40:46,139 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:40:46,154 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:40:46,203 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:40:46,204 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:40:46,515 628 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:40:46,656 769 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (141ms total) [0 unknowns]\n2025-12-09 02:40:46,688 801 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:40:47,044 1157 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:40:47,239 1352 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:40:47,242 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:40:47,242 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:40:47,242 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:40:47,242 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:40:47,243 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:40:47,243 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:40:47,587 1700 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:40:47,599 1712 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:40:47,602 1715 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:40:47,737 1850 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:40:47,747 1860 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:40:47,757 1870 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:47,765 1878 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:47,770 1883 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:40:47,779 1892 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:47,789 1902 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:47,814 1927 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:40:47,850 1963 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4856\n2025-12-09 02:40:47,862 1975 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:47,865 1978 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:47,865 1978 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.527\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:40:42,412 INFO [ omero.gateway] (MainThread) created connection (uuid=71ee4278-bf9c-467f-a5b5-984ac430d322) I2025-12-09 02:40:42,471 INFO [ omero.gateway] (MainThread) created connection (uuid=778f6799-ad2b-48bd-a6ab-a4d2ade8ec4d) 2025-12-09 02:40:48,019 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=71ee4278-bf9c-467f-a5b5-984ac430d322) INFO omero.gateway:__init__.py:2307 created connection (uuid=778f6799-ad2b-48bd-a6ab-a4d2ade8ec4d) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _________ ERROR at setup of TestRDefs.testQuantizationSettingsInvalid __________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 8ec318ed-8ec5-4e6f-acae-52ee0498447b -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:40:52,642 240 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:40:52,657 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:40:52,704 302 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:40:52,705 303 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:40:53,009 607 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:40:53,147 745 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (138ms total) [0 unknowns]\n2025-12-09 02:40:53,177 775 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:40:53,527 1125 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:40:53,719 1317 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:40:53,723 1321 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:40:53,723 1321 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:40:53,723 1321 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:40:53,723 1321 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:40:53,723 1321 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:40:53,723 1321 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:40:54,059 1657 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:40:54,071 1669 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:40:54,074 1672 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:40:54,211 1809 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:40:54,220 1818 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:40:54,230 1828 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:54,239 1837 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:40:54,243 1841 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:40:54,253 1851 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:54,263 1861 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:40:54,287 1885 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:40:54,322 1920 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4860\n2025-12-09 02:40:54,333 1931 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:54,336 1934 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:40:54,336 1934 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.518\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:40:48,100 INFO [ omero.gateway] (MainThread) created connection (uuid=37eccab7-2eb8-4b19-b835-c96f9d783159) I2025-12-09 02:40:48,160 INFO [ omero.gateway] (MainThread) created connection (uuid=8ec318ed-8ec5-4e6f-acae-52ee0498447b) 2025-12-09 02:40:54,482 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=37eccab7-2eb8-4b19-b835-c96f9d783159) INFO omero.gateway:__init__.py:2307 created connection (uuid=8ec318ed-8ec5-4e6f-acae-52ee0498447b) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ___________ ERROR at setup of TestRDefs.testQuantizationSettingsBulk ___________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 177789bb-6337-4338-bfd7-e1ccab22e000 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:40:58,951 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:40:58,966 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:40:59,014 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:40:59,015 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:40:59,319 609 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:40:59,456 746 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (137ms total) [0 unknowns]\n2025-12-09 02:40:59,487 777 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:40:59,838 1128 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:41:00,035 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:41:00,039 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:41:00,039 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:41:00,040 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:41:00,040 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:41:00,040 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:41:00,040 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:41:00,400 1690 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:41:00,413 1703 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:41:00,416 1706 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:41:00,553 1843 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:41:00,563 1853 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:41:00,573 1863 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:00,582 1872 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:00,587 1877 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:41:00,598 1888 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:00,608 1898 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:00,657 1947 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:41:00,695 1985 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4864\n2025-12-09 02:41:00,705 1995 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:00,707 1997 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:00,708 1998 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.557\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:40:54,562 INFO [ omero.gateway] (MainThread) created connection (uuid=55893b62-8329-4d62-a4d8-e5ad5237a3a9) I2025-12-09 02:40:54,622 INFO [ omero.gateway] (MainThread) created connection (uuid=177789bb-6337-4338-bfd7-e1ccab22e000) 2025-12-09 02:41:00,864 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=55893b62-8329-4d62-a4d8-e5ad5237a3a9) INFO omero.gateway:__init__.py:2307 created connection (uuid=177789bb-6337-4338-bfd7-e1ccab22e000) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _______________ ERROR at setup of TestRDefs.testGetChannelsNoRE ________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 6fdd55e3-e57f-4250-ad70-101e2453d544 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:41:05,441 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:41:05,456 264 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:41:05,504 312 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:41:05,506 314 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:41:05,814 622 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:41:05,955 763 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (142ms total) [0 unknowns]\n2025-12-09 02:41:05,986 794 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:41:06,350 1158 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:41:06,550 1358 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:41:06,555 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:41:06,555 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:41:06,555 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:41:06,555 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:41:06,555 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:41:06,555 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:41:06,893 1701 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:41:06,906 1714 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:41:06,909 1717 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:41:07,055 1863 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:41:07,064 1872 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:41:07,075 1883 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:07,084 1892 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:07,089 1897 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:41:07,098 1906 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:07,108 1916 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:07,134 1942 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:41:07,174 1982 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4868\n2025-12-09 02:41:07,183 1991 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:07,186 1994 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:07,186 1994 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.533\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:41:00,947 INFO [ omero.gateway] (MainThread) created connection (uuid=94302d13-eb10-4921-bf80-1f39c2f91fcb) I2025-12-09 02:41:01,008 INFO [ omero.gateway] (MainThread) created connection (uuid=6fdd55e3-e57f-4250-ad70-101e2453d544) 2025-12-09 02:41:07,329 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=94302d13-eb10-4921-bf80-1f39c2f91fcb) INFO omero.gateway:__init__.py:2307 created connection (uuid=6fdd55e3-e57f-4250-ad70-101e2453d544) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ____________ ERROR at setup of TestRDefs.testSetActiveChannelsNoRE _____________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 0a46c64c-c0db-454a-aeca-1f2962506cfe -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:41:11,863 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:41:11,879 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:41:11,928 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:41:11,929 319 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:41:12,239 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:41:12,380 770 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (140ms total) [0 unknowns]\n2025-12-09 02:41:12,412 802 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:41:12,791 1181 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:41:12,998 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:41:13,003 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:41:13,003 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:41:13,003 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:41:13,003 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:41:13,003 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:41:13,003 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:41:13,339 1729 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:41:13,353 1743 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:41:13,356 1746 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:41:13,494 1884 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:41:13,504 1894 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:41:13,514 1904 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:13,523 1913 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:13,528 1918 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:41:13,538 1928 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:13,547 1937 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:13,572 1962 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:41:13,610 2000 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4872\n2025-12-09 02:41:13,621 2011 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:13,624 2014 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:13,624 2014 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.523\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:41:07,411 INFO [ omero.gateway] (MainThread) created connection (uuid=b1fd19de-4efb-453d-958e-46991ed4fd8a) I2025-12-09 02:41:07,469 INFO [ omero.gateway] (MainThread) created connection (uuid=0a46c64c-c0db-454a-aeca-1f2962506cfe) 2025-12-09 02:41:13,768 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=b1fd19de-4efb-453d-958e-46991ed4fd8a) INFO omero.gateway:__init__.py:2307 created connection (uuid=0a46c64c-c0db-454a-aeca-1f2962506cfe) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ___________ ERROR at setup of TestRDefs.testSetActiveChannelsWithRE ____________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 2f28f9c5-08e7-42e7-81e5-8b8664ffd04d -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:41:17,570 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:41:17,585 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:41:17,634 317 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:41:17,635 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:41:17,947 630 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:41:18,089 772 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (142ms total) [0 unknowns]\n2025-12-09 02:41:18,121 804 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:41:18,486 1169 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:41:18,684 1367 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:41:18,687 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:41:18,687 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:41:18,688 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:41:18,688 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:41:18,688 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:41:18,688 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:41:19,029 1712 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:41:19,042 1725 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:41:19,045 1728 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:41:19,181 1864 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:41:19,190 1873 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:41:19,199 1882 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:19,208 1891 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:19,213 1896 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:41:19,222 1905 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:19,230 1913 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:19,254 1937 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:41:19,290 1973 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4876\n2025-12-09 02:41:19,300 1983 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:19,303 1986 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:19,303 1986 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.518\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:41:13,849 INFO [ omero.gateway] (MainThread) created connection (uuid=933adb90-abaa-43af-9a6b-39c440bdc4c9) I2025-12-09 02:41:13,906 INFO [ omero.gateway] (MainThread) created connection (uuid=2f28f9c5-08e7-42e7-81e5-8b8664ffd04d) 2025-12-09 02:41:19,457 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=933adb90-abaa-43af-9a6b-39c440bdc4c9) INFO omero.gateway:__init__.py:2307 created connection (uuid=2f28f9c5-08e7-42e7-81e5-8b8664ffd04d) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ___ ERROR at setup of TestRDefs.test_set_active_channels_set_inactive[True] ____ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 0d532889-518e-4a10-8827-8f90ab727071 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:41:24,129 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:41:24,144 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:41:24,192 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:41:24,193 306 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:41:24,495 608 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:41:24,632 745 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (136ms total) [0 unknowns]\n2025-12-09 02:41:24,662 775 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:41:25,023 1136 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:41:25,216 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:41:25,220 1333 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:41:25,220 1333 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:41:25,220 1333 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:41:25,220 1333 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:41:25,220 1333 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:41:25,220 1333 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:41:25,557 1670 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:41:25,569 1682 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:41:25,572 1685 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:41:25,711 1824 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:41:25,721 1834 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:41:25,731 1844 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:25,740 1853 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:25,745 1858 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:41:25,754 1867 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:25,764 1877 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:25,788 1901 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:41:25,824 1937 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4880\n2025-12-09 02:41:25,833 1946 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:25,836 1949 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:25,836 1949 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.522\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:41:19,540 INFO [ omero.gateway] (MainThread) created connection (uuid=169e5650-a795-40e2-b247-98236b30d43e) I2025-12-09 02:41:19,598 INFO [ omero.gateway] (MainThread) created connection (uuid=0d532889-518e-4a10-8827-8f90ab727071) 2025-12-09 02:41:25,996 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=169e5650-a795-40e2-b247-98236b30d43e) INFO omero.gateway:__init__.py:2307 created connection (uuid=0d532889-518e-4a10-8827-8f90ab727071) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ___ ERROR at setup of TestRDefs.test_set_active_channels_set_inactive[False] ___ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 258a1e33-099b-46f8-819c-38e5731b1357 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:41:30,383 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:41:30,398 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:41:30,446 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:41:30,447 306 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:41:30,747 606 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:41:30,885 744 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 135ms. (138ms total) [0 unknowns]\n2025-12-09 02:41:30,916 775 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:41:31,271 1130 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:41:31,463 1322 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:41:31,467 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:41:31,467 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:41:31,467 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:41:31,467 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:41:31,467 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:41:31,467 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:41:31,802 1661 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:41:31,814 1673 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:41:31,818 1677 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:41:31,959 1818 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:41:31,969 1828 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:41:31,979 1838 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:31,987 1846 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:31,991 1850 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:41:32,000 1859 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:32,009 1868 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:32,033 1892 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:41:32,070 1929 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4884\n2025-12-09 02:41:32,083 1942 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:32,086 1945 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:32,086 1945 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.524\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:41:26,078 INFO [ omero.gateway] (MainThread) created connection (uuid=c20f1001-0a44-41e2-9a70-e80a7ac513d9) I2025-12-09 02:41:26,136 INFO [ omero.gateway] (MainThread) created connection (uuid=258a1e33-099b-46f8-819c-38e5731b1357) 2025-12-09 02:41:32,240 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=c20f1001-0a44-41e2-9a70-e80a7ac513d9) INFO omero.gateway:__init__.py:2307 created connection (uuid=258a1e33-099b-46f8-819c-38e5731b1357) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ______________ ERROR at setup of TestRDefs.testUnregisterService _______________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 6248d43b-71cc-4440-ac20-1d2660c37a34 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:41:36,680 254 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:41:36,695 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:41:36,745 319 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:41:36,746 320 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:41:37,059 633 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:41:37,200 774 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 139ms. (142ms total) [0 unknowns]\n2025-12-09 02:41:37,233 807 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:41:37,593 1167 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:41:37,799 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:41:37,802 1376 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:41:37,802 1376 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:41:37,803 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:41:37,803 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:41:37,803 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:41:37,803 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:41:38,133 1707 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:41:38,145 1719 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:41:38,148 1722 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:41:38,286 1860 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:41:38,295 1869 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:41:38,305 1879 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:38,313 1887 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:38,318 1892 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:41:38,327 1901 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:38,336 1910 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:38,359 1933 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:41:38,395 1969 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4888\n2025-12-09 02:41:38,405 1979 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:38,408 1982 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:38,408 1982 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.515\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:41:32,322 INFO [ omero.gateway] (MainThread) created connection (uuid=70adfd1e-101d-4434-8d83-d6f2be629c3c) I2025-12-09 02:41:32,381 INFO [ omero.gateway] (MainThread) created connection (uuid=6248d43b-71cc-4440-ac20-1d2660c37a34) 2025-12-09 02:41:38,562 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=70adfd1e-101d-4434-8d83-d6f2be629c3c) INFO omero.gateway:__init__.py:2307 created connection (uuid=6248d43b-71cc-4440-ac20-1d2660c37a34) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _______________ ERROR at setup of TestRDefs.testRegisterService ________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k d073bab1-9d07-43d6-bda7-a77067e21f7a -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:41:43,131 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:41:43,146 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:41:43,193 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:41:43,194 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:41:43,497 607 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:41:43,633 743 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (136ms total) [0 unknowns]\n2025-12-09 02:41:43,664 774 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:41:44,013 1123 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:41:44,207 1317 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:41:44,210 1320 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:41:44,210 1320 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:41:44,210 1320 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:41:44,210 1320 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:41:44,210 1320 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:41:44,210 1320 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:41:44,542 1652 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:41:44,554 1664 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:41:44,557 1667 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:41:44,695 1805 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:41:44,704 1814 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:41:44,714 1824 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:44,724 1834 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:44,728 1838 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:41:44,738 1848 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:44,746 1856 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:44,769 1879 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:41:44,804 1914 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4892\n2025-12-09 02:41:44,817 1927 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:44,820 1930 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:44,820 1930 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.518\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:41:38,648 INFO [ omero.gateway] (MainThread) created connection (uuid=4989c964-8b29-44f1-8cac-f39312348ec7) I2025-12-09 02:41:38,708 INFO [ omero.gateway] (MainThread) created connection (uuid=d073bab1-9d07-43d6-bda7-a77067e21f7a) 2025-12-09 02:41:44,976 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=4989c964-8b29-44f1-8cac-f39312348ec7) INFO omero.gateway:__init__.py:2307 created connection (uuid=d073bab1-9d07-43d6-bda7-a77067e21f7a) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ___________________ ERROR at setup of TestRDefs.testCloseRE ____________________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k ab421dba-b3fb-481b-ba21-97ad64779270 -p 14064 import -d 1074 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:41:48,741 240 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:41:48,756 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:41:48,803 302 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:41:48,804 303 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:41:49,105 604 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:41:49,242 741 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (137ms total) [0 unknowns]\n2025-12-09 02:41:49,273 772 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:41:49,624 1123 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:41:49,819 1318 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:41:49,823 1322 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:41:49,823 1322 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:41:49,823 1322 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:41:49,823 1322 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:41:49,823 1322 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:41:49,823 1322 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:41:50,168 1667 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1074\n2025-12-09 02:41:50,180 1679 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1074\n2025-12-09 02:41:50,183 1682 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:41:50,322 1821 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:41:50,331 1830 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:41:50,341 1840 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:50,350 1849 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:41:50,355 1854 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:41:50,364 1863 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:50,372 1871 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:41:50,396 1895 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:41:50,433 1932 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4896\n2025-12-09 02:41:50,442 1941 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:50,445 1944 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:41:50,445 1944 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.527\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:41:45,058 INFO [ omero.gateway] (MainThread) created connection (uuid=cf0bcdca-6aa9-4fcd-bf7b-70ae929dabf8) I2025-12-09 02:41:45,115 INFO [ omero.gateway] (MainThread) created connection (uuid=ab421dba-b3fb-481b-ba21-97ad64779270) 2025-12-09 02:41:50,604 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2307 created connection (uuid=cf0bcdca-6aa9-4fcd-bf7b-70ae929dabf8) INFO omero.gateway:__init__.py:2307 created connection (uuid=ab421dba-b3fb-481b-ba21-97ad64779270) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _____________ ERROR at setup of TestWrapper.testAllObjectsWrapped ______________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 27f3eaff-9fb0-4f6f-bb4b-7031dd6b14fa -p 14064 import -d 1089 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:43:40,783 243 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:43:40,798 258 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:43:40,847 307 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:43:40,848 308 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:43:41,152 612 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:43:41,288 748 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 134ms. (136ms total) [0 unknowns]\n2025-12-09 02:43:41,319 779 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:43:41,677 1137 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:43:41,884 1344 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:43:41,894 1354 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:43:41,894 1354 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:43:41,894 1354 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:43:41,894 1354 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:43:41,894 1354 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:43:41,894 1354 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:43:42,236 1696 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1089\n2025-12-09 02:43:42,249 1709 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1089\n2025-12-09 02:43:42,253 1713 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:43:42,409 1869 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:43:42,419 1879 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:43:42,431 1891 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:43:42,442 1902 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:43:42,446 1906 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:43:42,456 1916 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:43:42,466 1926 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:43:42,499 1959 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:43:42,536 1996 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4905\n2025-12-09 02:43:42,555 2015 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:43:42,558 2018 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:43:42,558 2018 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.571\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:43:35,063 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:35,068 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:35,101 INFO [ omero.gateway] (MainThread) created connection (uuid=4c44fe47-2755-4021-9fef-98fc304d591b) 2025-12-09 02:43:35,532 INFO [ omero.gateway] (MainThread) created connection (uuid=3dff356e-633e-47ed-bdf7-f9356efd6022) 2025-12-09 02:43:35,565 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:35,598 INFO [ omero.gateway] (MainThread) created connection (uuid=82118d99-532c-4f47-8599-88d230520589) 2025-12-09 02:43:35,631 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:35,665 INFO [ omero.gateway] (MainThread) created connection (uuid=c908a2a3-be64-4c2b-bb67-48c845508a98) 2025-12-09 02:43:35,701 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:35,736 INFO [ omero.gateway] (MainThread) created connection (uuid=c6b0b470-b387-4065-b740-56a88fbc9653) 2025-12-09 02:43:35,774 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:35,808 INFO [ omero.gateway] (MainThread) created connection (uuid=1135e457-d14d-4074-bd76-b84190bafc42) 2025-12-09 02:43:35,844 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:35,877 INFO [ omero.gateway] (MainThread) created connection (uuid=a39ee1be-7f22-41d1-9af9-375d226a72a9) 2025-12-09 02:43:35,913 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:35,946 INFO [ omero.gateway] (MainThread) created connection (uuid=43a6038d-adb1-4c83-975b-1d1279c72bb5) 2025-12-09 02:43:35,989 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:36,024 INFO [ omero.gateway] (MainThread) created connection (uuid=98399d34-8829-4bdd-9bdf-26b26ee1651c) 2025-12-09 02:43:36,070 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:36,105 INFO [ omero.gateway] (MainThread) created connection (uuid=4461410d-9cf9-4c2b-82b0-2d0711cf4ba9) 2025-12-09 02:43:36,153 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:36,156 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:36,193 INFO [ omero.gateway] (MainThread) created connection (uuid=26ff7911-76ad-4eb7-9492-e5df093b643d) 2025-12-09 02:43:36,259 INFO [ omero.gateway] (MainThread) created connection (uuid=618ff251-b772-4b6c-895c-2008fafaeda7) I2025-12-09 02:43:36,319 INFO [ omero.gateway] (MainThread) created connection (uuid=27f3eaff-9fb0-4f6f-bb4b-7031dd6b14fa) 2025-12-09 02:43:42,704 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=4c44fe47-2755-4021-9fef-98fc304d591b) INFO omero.gateway:__init__.py:2307 created connection (uuid=3dff356e-633e-47ed-bdf7-f9356efd6022) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=82118d99-532c-4f47-8599-88d230520589) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=c908a2a3-be64-4c2b-bb67-48c845508a98) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=c6b0b470-b387-4065-b740-56a88fbc9653) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=1135e457-d14d-4074-bd76-b84190bafc42) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=a39ee1be-7f22-41d1-9af9-375d226a72a9) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=43a6038d-adb1-4c83-975b-1d1279c72bb5) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=98399d34-8829-4bdd-9bdf-26b26ee1651c) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=4461410d-9cf9-4c2b-82b0-2d0711cf4ba9) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=26ff7911-76ad-4eb7-9492-e5df093b643d) INFO omero.gateway:__init__.py:2307 created connection (uuid=618ff251-b772-4b6c-895c-2008fafaeda7) INFO omero.gateway:__init__.py:2307 created connection (uuid=27f3eaff-9fb0-4f6f-bb4b-7031dd6b14fa) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _______________ ERROR at setup of TestWrapper.testDatasetWrapper _______________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 332ed476-0f56-4470-ba73-36fa3b39be22 -p 14064 import -d 1089 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:43:48,077 255 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:43:48,092 270 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:43:48,142 320 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:43:48,143 321 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:43:48,455 633 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:43:48,597 775 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 139ms. (141ms total) [0 unknowns]\n2025-12-09 02:43:48,628 806 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:43:48,991 1169 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:43:49,185 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:43:49,189 1367 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:43:49,190 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:43:49,190 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:43:49,190 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:43:49,190 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:43:49,190 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:43:49,524 1702 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1089\n2025-12-09 02:43:49,537 1715 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1089\n2025-12-09 02:43:49,540 1718 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:43:49,680 1858 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:43:49,690 1868 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:43:49,701 1879 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:43:49,710 1888 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:43:49,714 1892 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:43:49,724 1902 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:43:49,733 1911 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:43:49,760 1938 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:43:49,797 1975 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4909\n2025-12-09 02:43:49,814 1992 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:43:49,817 1995 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:43:49,817 1995 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.531\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:43:43,526 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:43,563 INFO [ omero.gateway] (MainThread) created connection (uuid=5f914f5a-9336-4d42-afbf-c61827f397c0) 2025-12-09 02:43:43,630 INFO [ omero.gateway] (MainThread) created connection (uuid=98095098-9687-4499-ac8f-e806da5b961d) I2025-12-09 02:43:43,690 INFO [ omero.gateway] (MainThread) created connection (uuid=332ed476-0f56-4470-ba73-36fa3b39be22) 2025-12-09 02:43:49,965 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=5f914f5a-9336-4d42-afbf-c61827f397c0) INFO omero.gateway:__init__.py:2307 created connection (uuid=98095098-9687-4499-ac8f-e806da5b961d) INFO omero.gateway:__init__.py:2307 created connection (uuid=332ed476-0f56-4470-ba73-36fa3b39be22) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _______________ ERROR at setup of TestWrapper.testDetailsWrapper _______________ request = > gatewaywrapper = @pytest.fixture(scope='function') def author_testimg(request, gatewaywrapper): """ logs in as Author and returns the test image, creating it first if needed. """ gatewaywrapper.loginAsAuthor() > rv = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/pytest_fixtures.py:81: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ---------------------------- Captured stdout setup ----------------------------- omero -s localhost -k 7be9fcc3-95d6-4475-ad54-21f41295ccd1 -p 14064 import -d 1089 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:43:54,753 247 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:43:54,769 263 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:43:54,817 311 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:43:54,818 312 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:43:55,123 617 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:43:55,263 757 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (140ms total) [0 unknowns]\n2025-12-09 02:43:55,295 789 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:43:55,649 1143 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:43:55,849 1343 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:43:55,853 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:43:55,854 1348 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:43:55,854 1348 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:43:55,854 1348 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:43:55,854 1348 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:43:55,854 1348 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:43:56,198 1692 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1089\n2025-12-09 02:43:56,211 1705 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1089\n2025-12-09 02:43:56,214 1708 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:43:56,359 1853 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:43:56,369 1863 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:43:56,379 1873 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:43:56,388 1882 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:43:56,393 1887 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:43:56,403 1897 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:43:56,412 1906 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:43:56,439 1933 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:43:56,486 1980 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4913\n2025-12-09 02:43:56,491 1985 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:43:56,494 1988 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:43:56,494 1988 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.540\n') ---------------------------- Captured stderr setup ----------------------------- 2025-12-09 02:43:50,056 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:50,090 INFO [ omero.gateway] (MainThread) created connection (uuid=b3147fc0-d8cc-492d-a032-936303891ffc) 2025-12-09 02:43:50,159 INFO [ omero.gateway] (MainThread) created connection (uuid=8b277b73-ed4e-444b-810d-3622998b52c8) I2025-12-09 02:43:50,218 INFO [ omero.gateway] (MainThread) created connection (uuid=7be9fcc3-95d6-4475-ad54-21f41295ccd1) 2025-12-09 02:43:56,649 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=b3147fc0-d8cc-492d-a032-936303891ffc) INFO omero.gateway:__init__.py:2307 created connection (uuid=8b277b73-ed4e-444b-810d-3622998b52c8) INFO omero.gateway:__init__.py:2307 created connection (uuid=7be9fcc3-95d6-4475-ad54-21f41295ccd1) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) =================================== FAILURES =================================== ________ TestDownload.testPolicyGlobalRestriction[+read,+write,+image] _________ self = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testPolicyGlobalRestriction__r0') fixture = @pytest.mark.parametrize('fixture', POLICY_FIXTURES, ids=[str(x) for x in POLICY_FIXTURES]) def testPolicyGlobalRestriction(self, tmpdir, fixture): # Skip f this isn't a check for this particular # config, then skip. self.skip_if("omero.policy.binary_access", lambda x: x != fixture.cfg) group = self.new_group(perms='rwr---') > self.do_restrictions(fixture, tmpdir, group) test/integration/clitest/test_download.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_download.py:301: in do_restrictions images = self.import_fake_file(0, client=upper, plates=1, plateRows=1, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_05ndztjpl&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 1, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '0aefab47-fab3-463b-a2ff-58a7477d82e9' args = ['omero', '-s', 'localhost', '-k', '0aefab47-fab3-463b-a2ff-58a7477d82e9', '-p', ...] popen = out = b'' err = b'Joined session for 2081d0af-e14a-4c35-a9ad-e04e05759504@localhost:14064. Idle timeout: 10 min. Current group: d365c2...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.252\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '0aefab47-fab3-463b-a2ff-58a7477d82e9', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_05ndztjpl&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake')]] 2 E b'' E b'Joined session for 2081d0af-e14a-4c35-a9ad-e04e05759504@localhost:14064. Idle timeout: 10 min. Current group: d365c2f3-8d08-427b-a843-c0535eafc66f\n2025-12-09 02:07:23,720 243 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:07:23,735 258 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:07:23,782 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:07:23,783 306 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:07:23,783 306 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:07:23,784 307 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:07:23,784 307 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:07:23,784 307 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:07:24,090 613 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:07:24,262 785 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 170ms. (172ms total) [0 unknowns]\n2025-12-09 02:07:24,296 819 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:07:24,690 1213 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:07:24,898 1421 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:07:24,907 1430 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:07:24,907 1430 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:07:24,907 1430 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:07:24,907 1430 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:07:24,907 1430 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:07:24,907 1430 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:07:24,969 1492 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:07:25,107 1630 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:07:25,113 1636 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_05ndztjpl&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake...\n2025-12-09 02:07:25,123 1646 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_05ndztjpl&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:25,133 1656 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_05ndztjpl&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:25,158 1681 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:07:25,202 1725 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3663\n2025-12-09 02:07:25,213 1736 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_05ndztjpl&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:25,216 1739 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:25,216 1739 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.252\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _________ TestDownload.testPolicyGroupRestriction[+read,+write,+image] _________ self = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testPolicyGroupRestriction__re0') fixture = @pytest.mark.parametrize('fixture', POLICY_FIXTURES, ids=[str(x) for x in POLICY_FIXTURES]) def testPolicyGroupRestriction(self, tmpdir, fixture): parts = fixture.cfg.split(",") config = [NV("omero.policy.binary_access", x) for x in parts] group = self.new_group(perms='rwr---', config=config) > self.do_restrictions(fixture, tmpdir, group) test/integration/clitest/test_download.py:294: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_download.py:301: in do_restrictions images = self.import_fake_file(0, client=upper, plates=1, plateRows=1, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0xz5skwee&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 1, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '4bf90eca-96e3-46b4-8230-11fabdd0ff7f' args = ['omero', '-s', 'localhost', '-k', '4bf90eca-96e3-46b4-8230-11fabdd0ff7f', '-p', ...] popen = out = b'' err = b'Joined session for 97a63a67-153f-402a-a086-2285fbaff207@localhost:14064. Idle timeout: 10 min. Current group: 5d0c18...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.259\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '4bf90eca-96e3-46b4-8230-11fabdd0ff7f', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0xz5skwee&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake')]] 2 E b'' E b'Joined session for 97a63a67-153f-402a-a086-2285fbaff207@localhost:14064. Idle timeout: 10 min. Current group: 5d0c18ff-148b-4670-8206-1980d5452996\n2025-12-09 02:07:28,530 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:07:28,545 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:07:28,594 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:07:28,595 317 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:07:28,595 317 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:07:28,595 317 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:07:28,595 317 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:07:28,595 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:07:28,907 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:07:29,049 771 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (142ms total) [0 unknowns]\n2025-12-09 02:07:29,082 804 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:07:29,444 1166 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:07:29,646 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:07:29,651 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:07:29,651 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:07:29,651 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:07:29,651 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:07:29,651 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:07:29,651 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:07:29,715 1437 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:07:29,869 1591 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:07:29,875 1597 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0xz5skwee&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake...\n2025-12-09 02:07:29,886 1608 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0xz5skwee&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:29,896 1618 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0xz5skwee&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:29,919 1641 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:07:29,963 1685 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3669\n2025-12-09 02:07:29,965 1687 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0xz5skwee&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:29,968 1690 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:29,968 1690 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.259\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _____ TestDownload.testPolicyGroupRestriction[-read,-write,-image,-plate] ______ self = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testPolicyGroupRestriction__re1') fixture = @pytest.mark.parametrize('fixture', POLICY_FIXTURES, ids=[str(x) for x in POLICY_FIXTURES]) def testPolicyGroupRestriction(self, tmpdir, fixture): parts = fixture.cfg.split(",") config = [NV("omero.policy.binary_access", x) for x in parts] group = self.new_group(perms='rwr---', config=config) > self.do_restrictions(fixture, tmpdir, group) test/integration/clitest/test_download.py:294: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_download.py:301: in do_restrictions images = self.import_fake_file(0, client=upper, plates=1, plateRows=1, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0l_pmwi_z&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 1, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '52c7ec3b-9f7a-4027-a8de-614922620f94' args = ['omero', '-s', 'localhost', '-k', '52c7ec3b-9f7a-4027-a8de-614922620f94', '-p', ...] popen = out = b'' err = b'Joined session for 783ca543-3fed-45fd-9163-6c6881f797d2@localhost:14064. Idle timeout: 10 min. Current group: a15252...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.247\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '52c7ec3b-9f7a-4027-a8de-614922620f94', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0l_pmwi_z&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake')]] 2 E b'' E b'Joined session for 783ca543-3fed-45fd-9163-6c6881f797d2@localhost:14064. Idle timeout: 10 min. Current group: a15252c6-3a2c-4136-9119-bdb3953f1ebe\n2025-12-09 02:07:33,014 240 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:07:33,029 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:07:33,077 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:07:33,077 303 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:07:33,078 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:07:33,078 304 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:07:33,078 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:07:33,078 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:07:33,377 603 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:07:33,514 740 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 135ms. (137ms total) [0 unknowns]\n2025-12-09 02:07:33,546 772 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:07:33,900 1126 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:07:34,100 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:07:34,104 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:07:34,104 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:07:34,104 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:07:34,104 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:07:34,104 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:07:34,104 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:07:34,166 1392 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:07:34,307 1533 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:07:34,314 1540 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0l_pmwi_z&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake...\n2025-12-09 02:07:34,321 1547 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0l_pmwi_z&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:34,329 1555 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0l_pmwi_z&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:34,354 1580 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:07:34,402 1628 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3675\n2025-12-09 02:07:34,405 1631 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0l_pmwi_z&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:34,407 1633 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:34,408 1634 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.247\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _____ TestDownload.testPolicyGroupRestriction[-read,+write,+image,-plate] ______ self = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testPolicyGroupRestriction__re2') fixture = @pytest.mark.parametrize('fixture', POLICY_FIXTURES, ids=[str(x) for x in POLICY_FIXTURES]) def testPolicyGroupRestriction(self, tmpdir, fixture): parts = fixture.cfg.split(",") config = [NV("omero.policy.binary_access", x) for x in parts] group = self.new_group(perms='rwr---', config=config) > self.do_restrictions(fixture, tmpdir, group) test/integration/clitest/test_download.py:294: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_download.py:301: in do_restrictions images = self.import_fake_file(0, client=upper, plates=1, plateRows=1, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ahr9l1n4&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 1, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = 'abc69e1e-204b-4428-a7ef-23d9bb431c59' args = ['omero', '-s', 'localhost', '-k', 'abc69e1e-204b-4428-a7ef-23d9bb431c59', '-p', ...] popen = out = b'' err = b'Joined session for 6b843102-4d25-48c4-b781-e1729fb4230a@localhost:14064. Idle timeout: 10 min. Current group: 31f27d...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.263\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'abc69e1e-204b-4428-a7ef-23d9bb431c59', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ahr9l1n4&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake')]] 2 E b'' E b'Joined session for 6b843102-4d25-48c4-b781-e1729fb4230a@localhost:14064. Idle timeout: 10 min. Current group: 31f27dd0-8283-4faa-9920-72b94ac4faad\n2025-12-09 02:07:37,574 243 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:07:37,589 258 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:07:37,637 306 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:07:37,638 307 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:07:37,638 307 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:07:37,638 307 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:07:37,638 307 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:07:37,638 307 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:07:37,939 608 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:07:38,078 747 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (139ms total) [0 unknowns]\n2025-12-09 02:07:38,111 780 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:07:38,466 1135 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:07:38,663 1332 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:07:38,667 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:07:38,667 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:07:38,667 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:07:38,667 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:07:38,667 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:07:38,667 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:07:38,730 1399 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:07:38,883 1552 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:07:38,889 1558 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ahr9l1n4&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake...\n2025-12-09 02:07:38,900 1569 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ahr9l1n4&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:38,909 1578 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ahr9l1n4&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:38,935 1604 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:07:38,982 1651 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3681\n2025-12-09 02:07:38,985 1654 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ahr9l1n4&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:38,988 1657 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:38,988 1657 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.263\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _____ TestDownload.testPolicyGroupRestriction[+read,+write,+image,-plate] ______ self = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testPolicyGroupRestriction__re3') fixture = @pytest.mark.parametrize('fixture', POLICY_FIXTURES, ids=[str(x) for x in POLICY_FIXTURES]) def testPolicyGroupRestriction(self, tmpdir, fixture): parts = fixture.cfg.split(",") config = [NV("omero.policy.binary_access", x) for x in parts] group = self.new_group(perms='rwr---', config=config) > self.do_restrictions(fixture, tmpdir, group) test/integration/clitest/test_download.py:294: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_download.py:301: in do_restrictions images = self.import_fake_file(0, client=upper, plates=1, plateRows=1, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0yskgiw8r&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 1, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '1dfe714c-5b0b-4c14-b013-5f62569c953f' args = ['omero', '-s', 'localhost', '-k', '1dfe714c-5b0b-4c14-b013-5f62569c953f', '-p', ...] popen = out = b'' err = b'Joined session for bc4b85e3-e9fa-489e-971e-48db1694bdd3@localhost:14064. Idle timeout: 10 min. Current group: e7ab89...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.300\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '1dfe714c-5b0b-4c14-b013-5f62569c953f', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0yskgiw8r&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake')]] 2 E b'' E b'Joined session for bc4b85e3-e9fa-489e-971e-48db1694bdd3@localhost:14064. Idle timeout: 10 min. Current group: e7ab896e-abd6-4f22-8814-6ce2afc7a5c8\n2025-12-09 02:07:42,112 243 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:07:42,126 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:07:42,173 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:07:42,174 305 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:07:42,174 305 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:07:42,175 306 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:07:42,175 306 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:07:42,175 306 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:07:42,475 606 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:07:42,614 745 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 135ms. (138ms total) [0 unknowns]\n2025-12-09 02:07:42,646 777 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:07:42,999 1130 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:07:43,206 1337 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:07:43,211 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:07:43,211 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:07:43,211 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:07:43,211 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:07:43,211 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:07:43,211 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:07:43,275 1406 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:07:43,441 1572 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:07:43,448 1579 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0yskgiw8r&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake...\n2025-12-09 02:07:43,462 1593 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0yskgiw8r&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:43,472 1603 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0yskgiw8r&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:43,508 1639 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:07:43,563 1694 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3687\n2025-12-09 02:07:43,567 1698 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0yskgiw8r&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:43,570 1701 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:43,570 1701 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.300\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _____ TestDownload.testPolicyGroupRestriction[+read,+write,+image,+plate] ______ self = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testPolicyGroupRestriction__re4') fixture = @pytest.mark.parametrize('fixture', POLICY_FIXTURES, ids=[str(x) for x in POLICY_FIXTURES]) def testPolicyGroupRestriction(self, tmpdir, fixture): parts = fixture.cfg.split(",") config = [NV("omero.policy.binary_access", x) for x in parts] group = self.new_group(perms='rwr---', config=config) > self.do_restrictions(fixture, tmpdir, group) test/integration/clitest/test_download.py:294: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_download.py:301: in do_restrictions images = self.import_fake_file(0, client=upper, plates=1, plateRows=1, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0gnltwgta&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 1, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '15dfdade-80f5-4687-86aa-c52571f1fc47' args = ['omero', '-s', 'localhost', '-k', '15dfdade-80f5-4687-86aa-c52571f1fc47', '-p', ...] popen = out = b'' err = b'Joined session for 14d2a7ad-e4b4-4b85-9db3-18ac372b643a@localhost:14064. Idle timeout: 10 min. Current group: 82001f...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.318\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '15dfdade-80f5-4687-86aa-c52571f1fc47', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0gnltwgta&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake')]] 2 E b'' E b'Joined session for 14d2a7ad-e4b4-4b85-9db3-18ac372b643a@localhost:14064. Idle timeout: 10 min. Current group: 82001f58-a256-457c-b131-b8d264af8aa6\n2025-12-09 02:07:46,728 257 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:07:46,744 273 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:07:46,794 323 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:07:46,795 324 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:07:46,795 324 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:07:46,795 324 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:07:46,795 324 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:07:46,795 324 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:07:47,108 637 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:07:47,258 787 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 148ms. (150ms total) [0 unknowns]\n2025-12-09 02:07:47,292 821 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:07:47,665 1194 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:07:47,864 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:07:47,867 1396 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:07:47,867 1396 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:07:47,868 1397 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:07:47,868 1397 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:07:47,868 1397 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:07:47,868 1397 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:07:47,938 1467 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:07:48,076 1605 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:07:48,083 1612 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0gnltwgta&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake...\n2025-12-09 02:07:48,093 1622 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0gnltwgta&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:48,174 1703 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0gnltwgta&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:48,198 1727 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:07:48,243 1772 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3693\n2025-12-09 02:07:48,246 1775 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0gnltwgta&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:48,249 1778 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:48,249 1778 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.318\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _______________________ TestFS.testImportTime[all-True] ________________________ self = hcs = True, skip = 'all' capfd = <_pytest.capture.CaptureFixture object at 0x7f4995a08490> @pytest.mark.parametrize("hcs", [True, False]) @pytest.mark.parametrize("skip", ["all", "minmax", "thumbnails"]) def testImportTime(self, hcs, skip, capfd): kwargs = {} if hcs: kwargs["plateCols"] = 2 kwargs["plateRows"] = 2 kwargs["fields"] = 2 kwargs["images_count"] = 8 > images = self.import_fake_file(skip=skip, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_fs.py:140: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_82o_yo6dy&series=8&plateCols=2&plateRows=2&fields=2.fake') client = , extra_args = None skip = 'all', kwargs = {'fields': 2, 'plateCols': 2, 'plateRows': 2} server = 'localhost', port = '14064' key = 'ce69d5c2-f820-4c38-87b9-bb3f009cc56b' args = ['omero', '-s', 'localhost', '-k', 'ce69d5c2-f820-4c38-87b9-bb3f009cc56b', '-p', ...] popen = out = b'' err = b'Joined session for e22ad704-9b78-43a4-bedc-bd5b6f010b2a@localhost:14064. Idle timeout: 10 min. Current group: 6286f4...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.237\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'ce69d5c2-f820-4c38-87b9-bb3f009cc56b', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_82o_yo6dy&series=8&plateCols=2&plateRows=2&fields=2.fake')]] 2 E b'' E b'Joined session for e22ad704-9b78-43a4-bedc-bd5b6f010b2a@localhost:14064. Idle timeout: 10 min. Current group: 6286f4d5-541b-4b66-bc28-3f264ea96577\n2025-12-09 02:08:13,246 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:08:13,261 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:08:13,309 313 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:08:13,310 314 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:08:13,310 314 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:08:13,310 314 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:08:13,310 314 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:08:13,311 315 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:08:13,620 624 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:08:13,766 770 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 144ms. (147ms total) [0 unknowns]\n2025-12-09 02:08:13,799 803 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:08:14,157 1161 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:08:14,357 1361 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:08:14,362 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:08:14,362 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:08:14,362 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:08:14,362 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:08:14,362 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:08:14,362 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:08:14,424 1428 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:08:14,557 1561 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:08:14,564 1568 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_82o_yo6dy&series=8&plateCols=2&plateRows=2&fields=2.fake...\n2025-12-09 02:08:14,573 1577 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_82o_yo6dy&series=8&plateCols=2&plateRows=2&fields=2.fake\n2025-12-09 02:08:14,583 1587 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_82o_yo6dy&series=8&plateCols=2&plateRows=2&fields=2.fake\n2025-12-09 02:08:14,606 1610 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:08:14,650 1654 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3717\n2025-12-09 02:08:14,653 1657 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_82o_yo6dy&series=8&plateCols=2&plateRows=2&fields=2.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:08:14,656 1660 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:08:14,656 1660 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.237\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception ______________________ TestFS.testImportTime[minmax-True] ______________________ self = hcs = True, skip = 'minmax' capfd = <_pytest.capture.CaptureFixture object at 0x7f499f36d5d0> @pytest.mark.parametrize("hcs", [True, False]) @pytest.mark.parametrize("skip", ["all", "minmax", "thumbnails"]) def testImportTime(self, hcs, skip, capfd): kwargs = {} if hcs: kwargs["plateCols"] = 2 kwargs["plateRows"] = 2 kwargs["fields"] = 2 kwargs["images_count"] = 8 > images = self.import_fake_file(skip=skip, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_fs.py:140: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8kou3t36k&series=8&plateCols=2&plateRows=2&fields=2.fake') client = , extra_args = None skip = 'minmax', kwargs = {'fields': 2, 'plateCols': 2, 'plateRows': 2} server = 'localhost', port = '14064' key = 'ce69d5c2-f820-4c38-87b9-bb3f009cc56b' args = ['omero', '-s', 'localhost', '-k', 'ce69d5c2-f820-4c38-87b9-bb3f009cc56b', '-p', ...] popen = out = b'' err = b'Joined session for e22ad704-9b78-43a4-bedc-bd5b6f010b2a@localhost:14064. Idle timeout: 10 min. Current group: 6286f4...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.278\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'ce69d5c2-f820-4c38-87b9-bb3f009cc56b', '-p', '14064', 'import', '--skip', 'minmax', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8kou3t36k&series=8&plateCols=2&plateRows=2&fields=2.fake')]] 2 E b'' E b'Joined session for e22ad704-9b78-43a4-bedc-bd5b6f010b2a@localhost:14064. Idle timeout: 10 min. Current group: 6286f4d5-541b-4b66-bc28-3f264ea96577\n2025-12-09 02:08:19,112 240 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:08:19,127 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:08:19,175 303 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:08:19,175 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:08:19,176 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:08:19,475 603 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:08:19,618 746 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (143ms total) [0 unknowns]\n2025-12-09 02:08:19,650 778 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:08:20,004 1132 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:08:20,213 1341 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:08:20,218 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:08:20,218 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:08:20,218 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:08:20,219 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:08:20,219 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:08:20,219 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:08:20,317 1445 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:08:20,455 1583 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:08:20,465 1593 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8kou3t36k&series=8&plateCols=2&plateRows=2&fields=2.fake...\n2025-12-09 02:08:20,474 1602 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8kou3t36k&series=8&plateCols=2&plateRows=2&fields=2.fake\n2025-12-09 02:08:20,510 1638 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8kou3t36k&series=8&plateCols=2&plateRows=2&fields=2.fake\n2025-12-09 02:08:20,535 1663 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:08:20,583 1711 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3723\n2025-12-09 02:08:20,585 1713 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8kou3t36k&series=8&plateCols=2&plateRows=2&fields=2.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:08:20,588 1716 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:08:20,588 1716 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.278\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception ____________________ TestFS.testImportTime[thumbnails-True] ____________________ self = hcs = True, skip = 'thumbnails' capfd = <_pytest.capture.CaptureFixture object at 0x7f4993b02550> @pytest.mark.parametrize("hcs", [True, False]) @pytest.mark.parametrize("skip", ["all", "minmax", "thumbnails"]) def testImportTime(self, hcs, skip, capfd): kwargs = {} if hcs: kwargs["plateCols"] = 2 kwargs["plateRows"] = 2 kwargs["fields"] = 2 kwargs["images_count"] = 8 > images = self.import_fake_file(skip=skip, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_fs.py:140: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8k_3bxeq0&series=8&plateCols=2&plateRows=2&fields=2.fake') client = , extra_args = None skip = 'thumbnails', kwargs = {'fields': 2, 'plateCols': 2, 'plateRows': 2} server = 'localhost', port = '14064' key = 'ce69d5c2-f820-4c38-87b9-bb3f009cc56b' args = ['omero', '-s', 'localhost', '-k', 'ce69d5c2-f820-4c38-87b9-bb3f009cc56b', '-p', ...] popen = out = b'' err = b'Joined session for e22ad704-9b78-43a4-bedc-bd5b6f010b2a@localhost:14064. Idle timeout: 10 min. Current group: 6286f4...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.246\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'ce69d5c2-f820-4c38-87b9-bb3f009cc56b', '-p', '14064', 'import', '--skip', 'thumbnails', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8k_3bxeq0&series=8&plateCols=2&plateRows=2&fields=2.fake')]] 2 E b'' E b'Joined session for e22ad704-9b78-43a4-bedc-bd5b6f010b2a@localhost:14064. Idle timeout: 10 min. Current group: 6286f4d5-541b-4b66-bc28-3f264ea96577\n2025-12-09 02:08:25,281 256 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:08:25,297 272 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:08:25,347 322 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:08:25,347 322 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:08:25,348 323 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:08:25,660 635 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:08:25,809 784 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 146ms. (149ms total) [0 unknowns]\n2025-12-09 02:08:25,842 817 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:08:26,214 1189 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:08:26,413 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:08:26,417 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:08:26,417 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:08:26,417 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:08:26,417 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:08:26,417 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:08:26,417 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:08:26,520 1495 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:08:26,657 1632 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:08:26,666 1641 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8k_3bxeq0&series=8&plateCols=2&plateRows=2&fields=2.fake...\n2025-12-09 02:08:26,675 1650 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8k_3bxeq0&series=8&plateCols=2&plateRows=2&fields=2.fake\n2025-12-09 02:08:26,685 1660 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8k_3bxeq0&series=8&plateCols=2&plateRows=2&fields=2.fake\n2025-12-09 02:08:26,708 1683 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:08:26,753 1728 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3729\n2025-12-09 02:08:26,757 1732 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8k_3bxeq0&series=8&plateCols=2&plateRows=2&fields=2.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:08:26,759 1734 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:08:26,760 1735 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.246\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _________________ TestImport.testTargetArgument[source0-True] __________________ self = spw = True source = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testTargetArgument_source0_Tru0') capfd = <_pytest.capture.CaptureFixture object at 0x7f49799b5950> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("source", SOURCES) def testTargetArgument(self, spw, source, tmpdir, capfd): subdir = tmpdir for x in source.get_prefixes(): subdir = subdir.join(x) subdir.mkdir() if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:602: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:12:48,376 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:12:48,391 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:12:48,439 313 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:12:48,749 623 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:12:48,892 766 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (143ms total) [0 unknowns] 2025-12-09 02:12:48,925 799 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:12:49,288 1162 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:12:49,495 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:12:49,501 1375 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:12:49,501 1375 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:12:49,501 1375 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:12:49,501 1375 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:12:49,501 1375 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:12:49,501 1375 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:12:49,829 1703 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:95 2025-12-09 02:12:49,842 1716 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Screen:95 2025-12-09 02:12:49,845 1719 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:12:49,977 1851 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:12:49,987 1861 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testTargetArgument_source0_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:12:49,997 1871 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source0_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:12:50,006 1880 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source0_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:12:50,030 1904 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:12:50,069 1943 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3841 2025-12-09 02:12:50,077 1951 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source0_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:12:50,080 1954 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:12:50,080 1954 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.489 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _________________ TestImport.testTargetArgument[source1-True] __________________ self = spw = True source = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testTargetArgument_source1_Tru0') capfd = <_pytest.capture.CaptureFixture object at 0x7f49948b7150> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("source", SOURCES) def testTargetArgument(self, spw, source, tmpdir, capfd): subdir = tmpdir for x in source.get_prefixes(): subdir = subdir.join(x) subdir.mkdir() if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:602: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:12:55,462 244 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:12:55,477 259 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:12:55,525 307 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:12:55,829 611 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:12:55,967 749 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (138ms total) [0 unknowns] 2025-12-09 02:12:56,000 782 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:12:56,351 1133 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:12:56,546 1328 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:12:56,552 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:12:56,552 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:12:56,552 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:12:56,552 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:12:56,552 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:12:56,552 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:12:56,882 1664 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:96 2025-12-09 02:12:56,895 1677 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Screen:96 2025-12-09 02:12:56,898 1680 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:12:57,027 1809 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:12:57,037 1819 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testTargetArgument_source1_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:12:57,048 1830 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source1_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:12:57,058 1840 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source1_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:12:57,082 1864 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:12:57,118 1900 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3850 2025-12-09 02:12:57,128 1910 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source1_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:12:57,131 1913 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:12:57,131 1913 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.487 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _________________ TestImport.testTargetArgument[source2-True] __________________ self = spw = True source = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testTargetArgument_source2_Tru0') capfd = <_pytest.capture.CaptureFixture object at 0x7f499403eb10> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("source", SOURCES) def testTargetArgument(self, spw, source, tmpdir, capfd): subdir = tmpdir for x in source.get_prefixes(): subdir = subdir.join(x) subdir.mkdir() if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:602: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:13:02,621 240 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:13:02,636 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:13:02,686 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:13:03,003 622 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:13:03,150 769 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 143ms. (147ms total) [0 unknowns] 2025-12-09 02:13:03,184 803 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:13:03,552 1171 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:13:03,756 1375 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:13:03,762 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:13:03,762 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:13:03,762 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:13:03,763 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:13:03,763 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:13:03,763 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:13:04,101 1720 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:97 2025-12-09 02:13:04,114 1733 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Screen:97 2025-12-09 02:13:04,117 1736 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:13:04,253 1872 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:13:04,263 1882 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testTargetArgument_source2_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:13:04,274 1893 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source2_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:04,283 1902 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source2_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:04,308 1927 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:13:04,347 1966 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3859 2025-12-09 02:13:04,356 1975 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source2_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:04,359 1978 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:04,359 1978 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.503 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _________________ TestImport.testTargetArgument[source3-True] __________________ self = spw = True source = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testTargetArgument_source3_Tru0') capfd = <_pytest.capture.CaptureFixture object at 0x7f4993f8a010> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("source", SOURCES) def testTargetArgument(self, spw, source, tmpdir, capfd): subdir = tmpdir for x in source.get_prefixes(): subdir = subdir.join(x) subdir.mkdir() if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:602: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:13:09,836 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:13:09,850 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:13:09,898 303 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:13:10,201 606 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:13:10,341 746 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (140ms total) [0 unknowns] 2025-12-09 02:13:10,373 778 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:13:10,725 1130 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:13:10,941 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:13:10,946 1351 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:13:10,947 1352 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:13:10,947 1352 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:13:10,947 1352 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:13:10,947 1352 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:13:10,947 1352 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:13:11,270 1675 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:id:98 2025-12-09 02:13:11,283 1688 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Screen:98 2025-12-09 02:13:11,286 1691 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:13:11,428 1833 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:13:11,438 1843 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testTargetArgument_source3_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:13:11,447 1852 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source3_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:11,456 1861 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source3_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:11,480 1885 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:13:11,518 1923 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3868 2025-12-09 02:13:11,527 1932 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source3_Tru0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:11,530 1935 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:11,530 1935 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.495 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _________________ TestImport.testTargetArgument[source4-True] __________________ self = spw = True source = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testTargetArgument_source4_Tru0') capfd = <_pytest.capture.CaptureFixture object at 0x7f4994de6750> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("source", SOURCES) def testTargetArgument(self, spw, source, tmpdir, capfd): subdir = tmpdir for x in source.get_prefixes(): subdir = subdir.join(x) subdir.mkdir() if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:602: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:13:17,098 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:13:17,113 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:13:17,161 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:13:17,462 605 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:13:17,602 745 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (141ms total) [0 unknowns] 2025-12-09 02:13:17,634 777 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:13:17,990 1133 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:13:18,182 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:13:18,193 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:13:18,193 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:13:18,193 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:13:18,193 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:13:18,193 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:13:18,193 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:13:18,285 1428 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:(?.*) 2025-12-09 02:13:18,318 1461 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:13:18,456 1599 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:13:18,466 1609 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testTargetArgument_source4_Tru0/a/b/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:13:18,478 1621 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source4_Tru0/a/b/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:18,487 1630 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source4_Tru0/a/b/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:18,513 1656 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:13:18,551 1694 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3877 2025-12-09 02:13:18,563 1706 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source4_Tru0/a/b/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:18,566 1709 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:18,566 1709 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.285 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _________________ TestImport.testTargetArgument[source5-True] __________________ self = spw = True source = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testTargetArgument_source5_Tru0') capfd = <_pytest.capture.CaptureFixture object at 0x7f4994ac5490> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("source", SOURCES) def testTargetArgument(self, spw, source, tmpdir, capfd): subdir = tmpdir for x in source.get_prefixes(): subdir = subdir.join(x) subdir.mkdir() if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:602: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:13:23,665 244 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:13:23,680 259 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:13:23,731 310 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:13:24,039 618 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:13:24,179 758 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (139ms total) [0 unknowns] 2025-12-09 02:13:24,213 792 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:13:24,572 1151 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:13:24,767 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:13:24,772 1351 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:13:24,772 1351 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:13:24,772 1351 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:13:24,772 1351 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:13:24,772 1351 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:13:24,772 1351 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:13:24,871 1450 [ main] INFO ome.formats.importer.ImportConfig - Using import target: :(?.*) 2025-12-09 02:13:24,901 1480 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:13:25,036 1615 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:13:25,046 1625 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testTargetArgument_source5_Tru0/a/b/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:13:25,059 1638 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source5_Tru0/a/b/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:25,069 1648 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source5_Tru0/a/b/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:25,096 1675 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:13:25,133 1712 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3886 2025-12-09 02:13:25,143 1722 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testTargetArgument_source5_Tru0/a/b/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:25,150 1729 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:25,150 1729 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.282 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ____________ TestImport.testQualifiedNameModelTargetArgument[-True] ____________ self = spw = True, qualifier = '' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr0') capfd = <_pytest.capture.CaptureFixture object at 0x7f4994b95d50> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "%", "@")) def testQualifiedNameModelTargetArgument( self, spw, qualifier, tmpdir, capfd): source = self.NameModelTargetSource() subdir = tmpdir if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, qualifier, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:628: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:13:30,373 251 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:13:30,388 266 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:13:30,437 315 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:13:30,749 627 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:13:30,893 771 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 141ms. (144ms total) [0 unknowns] 2025-12-09 02:13:30,926 804 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:13:31,285 1163 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:13:31,481 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:13:31,486 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:13:31,486 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:13:31,486 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:13:31,486 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:13:31,487 1365 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:13:31,487 1365 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:13:31,827 1705 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:name:NameModelTargetSource-Test 2025-12-09 02:13:31,857 1735 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Screen:99 2025-12-09 02:13:31,860 1738 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:13:31,988 1866 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:13:31,998 1876 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:13:32,008 1886 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:32,017 1895 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:32,045 1923 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:13:32,077 1955 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3895 2025-12-09 02:13:32,089 1967 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:32,091 1969 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:32,092 1970 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.505 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ___________ TestImport.testQualifiedNameModelTargetArgument[+-True] ____________ self = spw = True, qualifier = '+' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr2') capfd = <_pytest.capture.CaptureFixture object at 0x7f497af10150> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "%", "@")) def testQualifiedNameModelTargetArgument( self, spw, qualifier, tmpdir, capfd): source = self.NameModelTargetSource() subdir = tmpdir if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, qualifier, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:628: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:13:37,603 254 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:13:37,618 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:13:37,667 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:13:37,980 631 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:13:38,124 775 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 142ms. (145ms total) [0 unknowns] 2025-12-09 02:13:38,157 808 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:13:38,522 1173 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:13:38,727 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:13:38,733 1384 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:13:38,734 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:13:38,734 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:13:38,734 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:13:38,734 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:13:38,734 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:13:39,064 1715 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:+name:NameModelTargetSource-Test 2025-12-09 02:13:39,080 1731 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Screen:99 2025-12-09 02:13:39,083 1734 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:13:39,217 1868 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:13:39,226 1877 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr2/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:13:39,235 1886 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr2/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:39,244 1895 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr2/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:39,267 1918 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:13:39,303 1954 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3904 2025-12-09 02:13:39,312 1963 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr2/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:39,315 1966 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:39,315 1966 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.491 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ___________ TestImport.testQualifiedNameModelTargetArgument[--True] ____________ self = spw = True, qualifier = '-' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr4') capfd = <_pytest.capture.CaptureFixture object at 0x7f497a958d10> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "%", "@")) def testQualifiedNameModelTargetArgument( self, spw, qualifier, tmpdir, capfd): source = self.NameModelTargetSource() subdir = tmpdir if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, qualifier, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:628: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:13:44,707 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:13:44,722 264 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:13:44,770 312 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:13:45,080 622 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:13:45,223 765 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 139ms. (142ms total) [0 unknowns] 2025-12-09 02:13:45,256 798 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:13:45,615 1157 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:13:45,814 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:13:45,818 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:13:45,818 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:13:45,819 1361 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:13:45,819 1361 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:13:45,819 1361 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:13:45,819 1361 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:13:46,165 1707 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:-name:NameModelTargetSource-Test 2025-12-09 02:13:46,182 1724 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Screen:99 2025-12-09 02:13:46,185 1727 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:13:46,315 1857 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:13:46,324 1866 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:13:46,334 1876 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:46,343 1885 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:46,367 1909 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:13:46,402 1944 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3913 2025-12-09 02:13:46,411 1953 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:46,414 1956 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:46,414 1956 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.498 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ___________ TestImport.testQualifiedNameModelTargetArgument[%-True] ____________ self = spw = True, qualifier = '%' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr6') capfd = <_pytest.capture.CaptureFixture object at 0x7f499447f5d0> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "%", "@")) def testQualifiedNameModelTargetArgument( self, spw, qualifier, tmpdir, capfd): source = self.NameModelTargetSource() subdir = tmpdir if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, qualifier, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:628: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:13:52,034 244 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:13:52,049 259 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:13:52,098 308 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:13:52,404 614 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:13:52,543 753 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (140ms total) [0 unknowns] 2025-12-09 02:13:52,576 786 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:13:52,930 1140 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:13:53,127 1337 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:13:53,132 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:13:53,132 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:13:53,132 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:13:53,132 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:13:53,132 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:13:53,132 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:13:53,469 1679 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:%name:NameModelTargetSource-Test 2025-12-09 02:13:53,487 1697 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Screen:99 2025-12-09 02:13:53,490 1700 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:13:53,621 1831 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:13:53,631 1841 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr6/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:13:53,641 1851 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr6/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:53,650 1860 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr6/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:13:53,675 1885 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:13:53,712 1922 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3922 2025-12-09 02:13:53,722 1932 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr6/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:53,724 1934 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:13:53,725 1935 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.504 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ___________ TestImport.testQualifiedNameModelTargetArgument[@-True] ____________ self = spw = True, qualifier = '@' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr8') capfd = <_pytest.capture.CaptureFixture object at 0x7f4994666ed0> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "%", "@")) def testQualifiedNameModelTargetArgument( self, spw, qualifier, tmpdir, capfd): source = self.NameModelTargetSource() subdir = tmpdir if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, qualifier, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:628: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:13:59,164 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:13:59,179 264 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:13:59,227 312 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:13:59,543 628 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:13:59,687 772 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 141ms. (144ms total) [0 unknowns] 2025-12-09 02:13:59,723 808 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:14:00,082 1167 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:14:00,283 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:14:00,288 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:14:00,288 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:14:00,288 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:14:00,288 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:14:00,288 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:14:00,288 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:14:00,621 1706 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:@name:NameModelTargetSource-Test 2025-12-09 02:14:00,649 1734 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Screen:100 2025-12-09 02:14:00,652 1737 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:14:00,785 1870 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:14:00,795 1880 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr8/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:14:00,805 1890 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr8/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:00,813 1898 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr8/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:00,838 1923 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:14:00,870 1955 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3931 2025-12-09 02:14:00,880 1965 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testQualifiedNameModelTargetAr8/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:00,883 1968 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:00,883 1968 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.504 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted __________ TestImport.testQualifiedNameTemplateTargetArgument[-True] ___________ self = spw = True, qualifier = '' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge0') capfd = <_pytest.capture.CaptureFixture object at 0x7f497aff7350> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "%", "@")) def testQualifiedNameTemplateTargetArgument( self, spw, qualifier, tmpdir, capfd): source = self.NameTemplateTargetSource() subdir = tmpdir if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, qualifier, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:654: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:14:06,405 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:14:06,420 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:14:06,467 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:14:06,769 606 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:14:06,909 746 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (140ms total) [0 unknowns] 2025-12-09 02:14:06,942 779 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:14:07,297 1134 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:14:07,531 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:14:07,536 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:14:07,537 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:14:07,537 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:14:07,537 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:14:07,537 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:14:07,537 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:14:07,640 1477 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:name:(?.*) 2025-12-09 02:14:07,670 1507 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:14:07,810 1647 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:14:07,820 1657 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:14:07,830 1667 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:07,839 1676 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:07,862 1699 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:14:07,903 1740 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3940 2025-12-09 02:14:07,911 1748 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:07,918 1755 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:07,918 1755 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.281 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted __________ TestImport.testQualifiedNameTemplateTargetArgument[+-True] __________ self = spw = True, qualifier = '+' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge2') capfd = <_pytest.capture.CaptureFixture object at 0x7f499486d9d0> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "%", "@")) def testQualifiedNameTemplateTargetArgument( self, spw, qualifier, tmpdir, capfd): source = self.NameTemplateTargetSource() subdir = tmpdir if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, qualifier, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:654: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:14:12,909 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:14:12,925 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:14:12,974 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:14:13,280 624 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:14:13,420 764 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (140ms total) [0 unknowns] 2025-12-09 02:14:13,452 796 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:14:13,804 1148 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:14:14,007 1351 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:14:14,012 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:14:14,012 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:14:14,012 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:14:14,012 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:14:14,012 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:14:14,012 1356 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:14:14,112 1456 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:+name:(?.*) 2025-12-09 02:14:14,142 1486 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:14:14,281 1625 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:14:14,291 1635 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge2/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:14:14,302 1646 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge2/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:14,311 1655 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge2/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:14,336 1680 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:14:14,373 1717 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3949 2025-12-09 02:14:14,383 1727 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge2/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:14,390 1734 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:14,390 1734 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.281 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted __________ TestImport.testQualifiedNameTemplateTargetArgument[--True] __________ self = spw = True, qualifier = '-' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge4') capfd = <_pytest.capture.CaptureFixture object at 0x7f4993f85c10> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "%", "@")) def testQualifiedNameTemplateTargetArgument( self, spw, qualifier, tmpdir, capfd): source = self.NameTemplateTargetSource() subdir = tmpdir if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, qualifier, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:654: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:14:19,373 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:14:19,389 266 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:14:19,438 315 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:14:19,750 627 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:14:19,896 773 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 143ms. (146ms total) [0 unknowns] 2025-12-09 02:14:19,930 807 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:14:20,302 1179 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:14:20,503 1380 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:14:20,508 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:14:20,508 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:14:20,508 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:14:20,508 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:14:20,508 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:14:20,508 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:14:20,600 1477 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:-name:(?.*) 2025-12-09 02:14:20,631 1508 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:14:20,772 1649 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:14:20,783 1660 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:14:20,792 1669 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:20,802 1679 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:20,826 1703 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:14:20,866 1743 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3958 2025-12-09 02:14:20,870 1747 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:20,873 1750 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:20,873 1750 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.276 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted __________ TestImport.testQualifiedNameTemplateTargetArgument[%-True] __________ self = spw = True, qualifier = '%' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge6') capfd = <_pytest.capture.CaptureFixture object at 0x7f4991b49a90> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "%", "@")) def testQualifiedNameTemplateTargetArgument( self, spw, qualifier, tmpdir, capfd): source = self.NameTemplateTargetSource() subdir = tmpdir if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, qualifier, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:654: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:14:26,025 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:14:26,040 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:14:26,089 314 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:14:26,399 624 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:14:26,542 767 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 141ms. (143ms total) [0 unknowns] 2025-12-09 02:14:26,575 800 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:14:26,931 1156 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:14:27,130 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:14:27,134 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:14:27,135 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:14:27,135 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:14:27,135 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:14:27,135 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:14:27,135 1360 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:14:27,234 1459 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:%name:(?.*) 2025-12-09 02:14:27,262 1487 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:14:27,396 1621 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:14:27,405 1630 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge6/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:14:27,415 1640 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge6/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:27,423 1648 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge6/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:27,446 1671 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:14:27,487 1712 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3967 2025-12-09 02:14:27,490 1715 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge6/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:27,492 1717 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:27,493 1718 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.262 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted __________ TestImport.testQualifiedNameTemplateTargetArgument[@-True] __________ self = spw = True, qualifier = '@' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge8') capfd = <_pytest.capture.CaptureFixture object at 0x7f499443ed90> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "%", "@")) def testQualifiedNameTemplateTargetArgument( self, spw, qualifier, tmpdir, capfd): source = self.NameTemplateTargetSource() subdir = tmpdir if spw: fakefile = subdir.join( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fakefile = subdir.join("test.fake") fakefile.write('') self.args += source.get_arg(self.client, qualifier, spw) self.args += [str(tmpdir)] # Now, run the import twice and check that the # pre and post container IDs match the sources' # assumptions > found1 = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:654: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:14:32,459 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:14:32,474 264 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:14:32,523 313 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:14:32,828 618 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:14:32,970 760 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (141ms total) [0 unknowns] 2025-12-09 02:14:33,002 792 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:14:33,361 1151 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:14:33,564 1354 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:14:33,569 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:14:33,569 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:14:33,569 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:14:33,569 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:14:33,569 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:14:33,569 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:14:33,661 1451 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:@name:(?.*) 2025-12-09 02:14:33,689 1479 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:14:33,842 1632 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:14:33,853 1643 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge8/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:14:33,862 1652 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge8/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:33,871 1661 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge8/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:33,894 1684 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:14:33,930 1720 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3976 2025-12-09 02:14:33,936 1726 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testQualifiedNameTemplateTarge8/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:33,943 1733 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:33,943 1733 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.285 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ________________ TestImport.testMultipleNameModelTargets[-True] ________________ self = spw = True, qualifier = '' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__0') capfd = <_pytest.capture.CaptureFixture object at 0x7f4979f0ead0> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-")) def testMultipleNameModelTargets(self, spw, qualifier, tmpdir, capfd): """ Test importing into a named target when Multiple targets exist """ name = "MultipleNameModelTargetSource-Test-" + self.uuid() oids = [] for i in range(2): if spw: kls = "Screen" else: kls = "Dataset" oid = self.create_object(kls, name=name) oids.append(oid) subdir = tmpdir if spw: fakefile = subdir.join(( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake")) else: fakefile = subdir.join("test.fake") fakefile.write('') target = "%s:%sname:%s" % (kls, qualifier, name) self.args += ['-T', target] self.args += [str(tmpdir)] # Run the import and get the container id > found = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:687: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:14:39,002 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:14:39,017 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:14:39,064 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:14:39,366 606 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:14:39,505 745 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (139ms total) [0 unknowns] 2025-12-09 02:14:39,538 778 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:14:39,892 1132 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:14:40,087 1327 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:14:40,092 1332 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:14:40,092 1332 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:14:40,092 1332 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:14:40,092 1332 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:14:40,092 1332 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:14:40,092 1332 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:14:40,424 1664 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:name:MultipleNameModelTargetSource-Test-1c596911-26f6-48a3-9c62-ee14f77637f7 2025-12-09 02:14:40,442 1682 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Screen:102 2025-12-09 02:14:40,444 1684 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:14:40,573 1813 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:14:40,583 1823 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:14:40,593 1833 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:40,602 1842 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:40,627 1867 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:14:40,661 1901 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3985 2025-12-09 02:14:40,672 1912 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__0/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:40,675 1915 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:40,675 1915 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.494 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _______________ TestImport.testMultipleNameModelTargets[+-True] ________________ self = spw = True, qualifier = '+' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__2') capfd = <_pytest.capture.CaptureFixture object at 0x7f4994e85850> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-")) def testMultipleNameModelTargets(self, spw, qualifier, tmpdir, capfd): """ Test importing into a named target when Multiple targets exist """ name = "MultipleNameModelTargetSource-Test-" + self.uuid() oids = [] for i in range(2): if spw: kls = "Screen" else: kls = "Dataset" oid = self.create_object(kls, name=name) oids.append(oid) subdir = tmpdir if spw: fakefile = subdir.join(( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake")) else: fakefile = subdir.join("test.fake") fakefile.write('') target = "%s:%sname:%s" % (kls, qualifier, name) self.args += ['-T', target] self.args += [str(tmpdir)] # Run the import and get the container id > found = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:687: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:14:43,715 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:14:43,730 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:14:43,778 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:14:44,083 610 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:14:44,221 748 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (138ms total) [0 unknowns] 2025-12-09 02:14:44,254 781 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:14:44,613 1140 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:14:44,803 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:14:44,812 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:14:44,813 1340 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:14:44,813 1340 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:14:44,813 1340 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:14:44,813 1340 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:14:44,813 1340 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:14:45,142 1669 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:+name:MultipleNameModelTargetSource-Test-caf76c50-fe5d-427d-8a7c-b43886a4edaf 2025-12-09 02:14:45,160 1687 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Screen:104 2025-12-09 02:14:45,163 1690 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:14:45,294 1821 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:14:45,304 1831 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__2/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:14:45,314 1841 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__2/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:45,322 1849 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__2/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:45,345 1872 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:14:45,381 1908 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3991 2025-12-09 02:14:45,389 1916 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__2/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:45,392 1919 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:45,392 1919 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.487 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _______________ TestImport.testMultipleNameModelTargets[--True] ________________ self = spw = True, qualifier = '-' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__4') capfd = <_pytest.capture.CaptureFixture object at 0x7f4994adcd10> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-")) def testMultipleNameModelTargets(self, spw, qualifier, tmpdir, capfd): """ Test importing into a named target when Multiple targets exist """ name = "MultipleNameModelTargetSource-Test-" + self.uuid() oids = [] for i in range(2): if spw: kls = "Screen" else: kls = "Dataset" oid = self.create_object(kls, name=name) oids.append(oid) subdir = tmpdir if spw: fakefile = subdir.join(( "SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake")) else: fakefile = subdir.join("test.fake") fakefile.write('') target = "%s:%sname:%s" % (kls, qualifier, name) self.args += ['-T', target] self.args += [str(tmpdir)] # Run the import and get the container id > found = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:687: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:14:48,644 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:14:48,660 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:14:48,709 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:14:49,022 631 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:14:49,167 776 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 142ms. (145ms total) [0 unknowns] 2025-12-09 02:14:49,201 810 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:14:49,561 1170 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:14:49,762 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:14:49,767 1376 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:14:49,767 1376 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:14:49,767 1376 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:14:49,767 1376 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:14:49,767 1376 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:14:49,767 1376 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:14:50,118 1727 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:-name:MultipleNameModelTargetSource-Test-a321cdcb-cab0-4201-818d-21f527be57f4 2025-12-09 02:14:50,135 1744 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Screen:105 2025-12-09 02:14:50,138 1747 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:14:50,268 1877 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:14:50,278 1887 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:14:50,287 1896 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:50,296 1905 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:50,322 1931 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:14:50,357 1966 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3997 2025-12-09 02:14:50,367 1976 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testMultipleNameModelTargets__4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:50,370 1979 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:50,370 1979 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.510 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ____________ TestImport.testNestedNameTemplateTargetArgument[True] _____________ self = spw = True tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNestedNameTemplateTargetAr0') capfd = <_pytest.capture.CaptureFixture object at 0x7f4994b85410> @pytest.mark.parametrize("spw", (True, False)) def testNestedNameTemplateTargetArgument( self, spw, tmpdir, capfd): outer = "NestedNameTemplateTargetArgument-Test-" + self.uuid() inner1 = "NestedNameTemplateTargetArgument-Test-" + self.uuid() inner2 = "NestedNameTemplateTargetArgument-Test-" + self.uuid() subdir = tmpdir.mkdir(outer) if spw: importType = "Plate" fake = ("SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: importType = "Image" fake = "test.fake" subdir.mkdir(inner1).join(fake).write('') subdir.mkdir(inner2).join(fake).write('') self.args += ("-T", "regex:name:^.*%s/(?.*)" % outer) self.args += [str(tmpdir)] # Now, run the import and check that two distinct # containers are created and used. > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:744: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:14:57,377 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:14:57,392 264 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:14:57,440 312 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:14:57,747 619 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:14:57,894 766 [ main] INFO ome.formats.importer.ImportCandidates - 2 file(s) parsed into 2 group(s) with 2 call(s) to setId in 143ms. (146ms total) [0 unknowns] 2025-12-09 02:14:57,926 798 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:14:58,316 1188 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:14:58,544 1416 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:14:58,548 1420 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:14:58,548 1420 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:14:58,548 1420 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:14:58,548 1420 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:14:58,549 1421 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:14:58,549 1421 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:14:58,650 1522 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:name:^.*NestedNameTemplateTargetArgument-Test-1f16b65a-16cd-40d1-9dbd-1de217ea0ddd/(?.*) 2025-12-09 02:14:58,651 1523 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:name:^.*NestedNameTemplateTargetArgument-Test-1f16b65a-16cd-40d1-9dbd-1de217ea0ddd/(?.*) 2025-12-09 02:14:58,679 1551 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:14:58,821 1693 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:14:58,831 1703 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNestedNameTemplateTargetAr0/NestedNameTemplateTargetArgument-Test-1f16b65a-16cd-40d1-9dbd-1de217ea0ddd/NestedNameTemplateTargetArgument-Test-951c524c-206d-4e9f-85bd-5fcc5cd241c4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:14:58,841 1713 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNestedNameTemplateTargetAr0/NestedNameTemplateTargetArgument-Test-1f16b65a-16cd-40d1-9dbd-1de217ea0ddd/NestedNameTemplateTargetArgument-Test-951c524c-206d-4e9f-85bd-5fcc5cd241c4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:58,849 1721 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNestedNameTemplateTargetAr0/NestedNameTemplateTargetArgument-Test-1f16b65a-16cd-40d1-9dbd-1de217ea0ddd/NestedNameTemplateTargetArgument-Test-951c524c-206d-4e9f-85bd-5fcc5cd241c4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:14:58,874 1746 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:14:58,909 1781 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4003 2025-12-09 02:14:58,918 1790 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNestedNameTemplateTargetAr0/NestedNameTemplateTargetArgument-Test-1f16b65a-16cd-40d1-9dbd-1de217ea0ddd/NestedNameTemplateTargetArgument-Test-951c524c-206d-4e9f-85bd-5fcc5cd241c4/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:58,925 1797 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:14:58,927 1799 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error 2025-12-09 02:14:58,927 1799 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Could not load target: ome.formats.importer.targets.TemplateImportTarget@bc12522 2025-12-09 02:14:58,927 1799 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.RuntimeException: Failed to load target at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:351) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: Ice.OperationInterruptedException: null at IceInternal.AsyncResultI.__wait(AsyncResultI.java:284) at omero.api.ServiceFactoryPrxHelper.end_getUpdateService(ServiceFactoryPrxHelper.java:5581) at omero.api.ServiceFactoryPrxHelper.getUpdateService(ServiceFactoryPrxHelper.java:5472) at omero.api.ServiceFactoryPrxHelper.getUpdateService(ServiceFactoryPrxHelper.java:5459) at ome.formats.importer.targets.TemplateImportTarget.load(TemplateImportTarget.java:73) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:334) ... 7 common frames omitted 2025-12-09 02:14:58,927 1799 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.279 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ___________ TestImport.testMultipleNameTemplateTargetArgument[-True] ___________ self = spw = True, qualifier = '' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget0') capfd = <_pytest.capture.CaptureFixture object at 0x7f4991b0d290> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "@")) def testMultipleNameTemplateTargetArgument( self, spw, qualifier, tmpdir, capfd): outer = "MultipleNameTemplateTargetArgument-Test-" + self.uuid() inner = "MultipleNameTemplateTargetArgument-Test-" + self.uuid() oids = [] for i in range(2): if spw: kls = "Screen" else: kls = "Dataset" oid = self.create_object(kls, name=inner) oids.append(oid) subdir = tmpdir.mkdir(outer) if spw: fake = ("SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fake = "test.fake" subdir.mkdir(inner).join(fake).write('') self.args += ("-T", ("regex:%sname:^.*%s/(?.*)" % (qualifier, outer))) self.args += [str(tmpdir)] # Now, run the import and check that the correct # container is used or created and used. > found = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:788: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:15:02,302 243 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:15:02,317 258 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:15:02,365 306 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:15:02,668 609 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:15:02,818 759 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 146ms. (149ms total) [0 unknowns] 2025-12-09 02:15:02,852 793 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:15:03,218 1159 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:15:03,424 1365 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:15:03,430 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:15:03,430 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:15:03,430 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:15:03,430 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:15:03,431 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:15:03,431 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:15:04,954 2895 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:name:^.*MultipleNameTemplateTargetArgument-Test-32b86e91-b2d5-4a02-814b-a3ff0b4b1c52/(?.*) 2025-12-09 02:15:04,984 2925 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:15:05,125 3066 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:15:05,135 3076 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget0/MultipleNameTemplateTargetArgument-Test-32b86e91-b2d5-4a02-814b-a3ff0b4b1c52/MultipleNameTemplateTargetArgument-Test-228eac13-583b-4444-a9cd-d1a1618ead63/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:15:05,144 3085 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget0/MultipleNameTemplateTargetArgument-Test-32b86e91-b2d5-4a02-814b-a3ff0b4b1c52/MultipleNameTemplateTargetArgument-Test-228eac13-583b-4444-a9cd-d1a1618ead63/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:15:05,154 3095 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget0/MultipleNameTemplateTargetArgument-Test-32b86e91-b2d5-4a02-814b-a3ff0b4b1c52/MultipleNameTemplateTargetArgument-Test-228eac13-583b-4444-a9cd-d1a1618ead63/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:15:05,178 3119 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:15:05,216 3157 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4012 2025-12-09 02:15:05,228 3169 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget0/MultipleNameTemplateTargetArgument-Test-32b86e91-b2d5-4a02-814b-a3ff0b4b1c52/MultipleNameTemplateTargetArgument-Test-228eac13-583b-4444-a9cd-d1a1618ead63/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:15:05,235 3176 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:15:05,235 3176 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.284 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted __________ TestImport.testMultipleNameTemplateTargetArgument[+-True] ___________ self = spw = True, qualifier = '+' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget2') capfd = <_pytest.capture.CaptureFixture object at 0x7f49940651d0> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "@")) def testMultipleNameTemplateTargetArgument( self, spw, qualifier, tmpdir, capfd): outer = "MultipleNameTemplateTargetArgument-Test-" + self.uuid() inner = "MultipleNameTemplateTargetArgument-Test-" + self.uuid() oids = [] for i in range(2): if spw: kls = "Screen" else: kls = "Dataset" oid = self.create_object(kls, name=inner) oids.append(oid) subdir = tmpdir.mkdir(outer) if spw: fake = ("SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fake = "test.fake" subdir.mkdir(inner).join(fake).write('') self.args += ("-T", ("regex:%sname:^.*%s/(?.*)" % (qualifier, outer))) self.args += [str(tmpdir)] # Now, run the import and check that the correct # container is used or created and used. > found = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:788: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:15:09,210 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:15:09,225 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:15:09,274 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:15:09,585 628 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:15:09,727 770 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 139ms. (142ms total) [0 unknowns] 2025-12-09 02:15:09,762 805 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:15:10,126 1169 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:15:10,332 1375 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:15:10,342 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:15:10,342 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:15:10,342 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:15:10,342 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:15:10,342 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:15:10,342 1385 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:15:10,435 1478 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:+name:^.*MultipleNameTemplateTargetArgument-Test-539e66b3-8e56-4ecb-afc3-e086e66b27e0/(?.*) 2025-12-09 02:15:10,463 1506 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:15:10,602 1645 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:15:10,612 1655 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget2/MultipleNameTemplateTargetArgument-Test-539e66b3-8e56-4ecb-afc3-e086e66b27e0/MultipleNameTemplateTargetArgument-Test-ec09df0d-646b-437e-83d7-fea872b00e5d/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:15:10,621 1664 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget2/MultipleNameTemplateTargetArgument-Test-539e66b3-8e56-4ecb-afc3-e086e66b27e0/MultipleNameTemplateTargetArgument-Test-ec09df0d-646b-437e-83d7-fea872b00e5d/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:15:10,630 1673 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget2/MultipleNameTemplateTargetArgument-Test-539e66b3-8e56-4ecb-afc3-e086e66b27e0/MultipleNameTemplateTargetArgument-Test-ec09df0d-646b-437e-83d7-fea872b00e5d/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:15:10,653 1696 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:15:10,691 1734 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4018 2025-12-09 02:15:10,699 1742 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget2/MultipleNameTemplateTargetArgument-Test-539e66b3-8e56-4ecb-afc3-e086e66b27e0/MultipleNameTemplateTargetArgument-Test-ec09df0d-646b-437e-83d7-fea872b00e5d/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:15:10,702 1745 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:15:10,702 1745 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.273 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted __________ TestImport.testMultipleNameTemplateTargetArgument[--True] ___________ self = spw = True, qualifier = '-' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget4') capfd = <_pytest.capture.CaptureFixture object at 0x7f4979e4f550> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "@")) def testMultipleNameTemplateTargetArgument( self, spw, qualifier, tmpdir, capfd): outer = "MultipleNameTemplateTargetArgument-Test-" + self.uuid() inner = "MultipleNameTemplateTargetArgument-Test-" + self.uuid() oids = [] for i in range(2): if spw: kls = "Screen" else: kls = "Dataset" oid = self.create_object(kls, name=inner) oids.append(oid) subdir = tmpdir.mkdir(outer) if spw: fake = ("SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fake = "test.fake" subdir.mkdir(inner).join(fake).write('') self.args += ("-T", ("regex:%sname:^.*%s/(?.*)" % (qualifier, outer))) self.args += [str(tmpdir)] # Now, run the import and check that the correct # container is used or created and used. > found = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:788: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:15:13,738 254 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:15:13,754 270 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:15:13,803 319 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:15:14,116 632 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:15:14,261 777 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 143ms. (146ms total) [0 unknowns] 2025-12-09 02:15:14,294 810 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:15:14,674 1190 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:15:14,883 1399 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:15:14,888 1404 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:15:14,888 1404 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:15:14,888 1404 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:15:14,888 1404 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:15:14,888 1404 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:15:14,888 1404 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:15:14,983 1499 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:-name:^.*MultipleNameTemplateTargetArgument-Test-944596fa-c5e6-4f01-9347-fa2c4afafd16/(?.*) 2025-12-09 02:15:15,012 1528 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:15:15,166 1682 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:15:15,176 1692 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget4/MultipleNameTemplateTargetArgument-Test-944596fa-c5e6-4f01-9347-fa2c4afafd16/MultipleNameTemplateTargetArgument-Test-8b36a979-731a-462b-b7b6-ea258dc8ce39/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:15:15,187 1703 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget4/MultipleNameTemplateTargetArgument-Test-944596fa-c5e6-4f01-9347-fa2c4afafd16/MultipleNameTemplateTargetArgument-Test-8b36a979-731a-462b-b7b6-ea258dc8ce39/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:15:15,197 1713 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget4/MultipleNameTemplateTargetArgument-Test-944596fa-c5e6-4f01-9347-fa2c4afafd16/MultipleNameTemplateTargetArgument-Test-8b36a979-731a-462b-b7b6-ea258dc8ce39/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:15:15,223 1739 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:15:15,260 1776 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4024 2025-12-09 02:15:15,267 1783 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget4/MultipleNameTemplateTargetArgument-Test-944596fa-c5e6-4f01-9347-fa2c4afafd16/MultipleNameTemplateTargetArgument-Test-8b36a979-731a-462b-b7b6-ea258dc8ce39/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:15:15,275 1791 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:15:15,275 1791 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.295 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted __________ TestImport.testMultipleNameTemplateTargetArgument[@-True] ___________ self = spw = True, qualifier = '@' tmpdir = local('/tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget6') capfd = <_pytest.capture.CaptureFixture object at 0x7f4993f9dfd0> @pytest.mark.parametrize("spw", (True, False)) @pytest.mark.parametrize("qualifier", ("", "+", "-", "@")) def testMultipleNameTemplateTargetArgument( self, spw, qualifier, tmpdir, capfd): outer = "MultipleNameTemplateTargetArgument-Test-" + self.uuid() inner = "MultipleNameTemplateTargetArgument-Test-" + self.uuid() oids = [] for i in range(2): if spw: kls = "Screen" else: kls = "Dataset" oid = self.create_object(kls, name=inner) oids.append(oid) subdir = tmpdir.mkdir(outer) if spw: fake = ("SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: fake = "test.fake" subdir.mkdir(inner).join(fake).write('') self.args += ("-T", ("regex:%sname:^.*%s/(?.*)" % (qualifier, outer))) self.args += [str(tmpdir)] # Now, run the import and check that the correct # container is used or created and used. > found = self.parse_container(spw, capfd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:788: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:567: in parse_container o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:15:18,466 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:15:18,482 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:15:18,530 313 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:15:18,837 620 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:15:18,983 766 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 144ms. (146ms total) [0 unknowns] 2025-12-09 02:15:19,016 799 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:15:19,380 1163 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:15:19,582 1365 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:15:19,588 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:15:19,588 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:15:19,588 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:15:19,589 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:15:19,589 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:15:19,589 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:15:19,683 1466 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:@name:^.*MultipleNameTemplateTargetArgument-Test-96ab2c26-49d1-4641-af9e-941a9c1e1df5/(?.*) 2025-12-09 02:15:19,712 1495 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:15:19,856 1639 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:15:19,866 1649 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget6/MultipleNameTemplateTargetArgument-Test-96ab2c26-49d1-4641-af9e-941a9c1e1df5/MultipleNameTemplateTargetArgument-Test-99585ca1-5bcb-43e3-b636-0950994255fb/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:15:19,875 1658 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget6/MultipleNameTemplateTargetArgument-Test-96ab2c26-49d1-4641-af9e-941a9c1e1df5/MultipleNameTemplateTargetArgument-Test-99585ca1-5bcb-43e3-b636-0950994255fb/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:15:19,884 1667 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget6/MultipleNameTemplateTargetArgument-Test-96ab2c26-49d1-4641-af9e-941a9c1e1df5/MultipleNameTemplateTargetArgument-Test-99585ca1-5bcb-43e3-b636-0950994255fb/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:15:19,909 1692 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:15:19,950 1733 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4030 2025-12-09 02:15:19,956 1739 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testMultipleNameTemplateTarget6/MultipleNameTemplateTargetArgument-Test-96ab2c26-49d1-4641-af9e-941a9c1e1df5/MultipleNameTemplateTargetArgument-Test-99585ca1-5bcb-43e3-b636-0950994255fb/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:15:19,963 1746 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:15:19,963 1746 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.282 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ________ TestImport.testUniqueMultipleNameTemplateTargetArgument[True] _________ self = spw = True tmpdir = local('/tmp/pytest-of-omero/pytest-60/testUniqueMultipleNameTemplate0') capfd = <_pytest.capture.CaptureFixture object at 0x7f496fd29dd0> @pytest.mark.parametrize("spw", (True, False)) def testUniqueMultipleNameTemplateTargetArgument( self, spw, tmpdir, capfd): outer = "UniqueMultipleNameTemplateTargetArgument-Test-" + self.uuid() inner = "UniqueMultipleNameTemplateTargetArgument-Test-" + self.uuid() oids = [] for i in range(2): if spw: kls = "Screen" else: kls = "Dataset" oid = self.create_object(kls, name=inner) oids.append(oid) subdir = tmpdir.mkdir(outer) if spw: importType = "Plate" fake = ("SPW&screens=0&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") else: importType = "Image" fake = "test.fake" subdir.mkdir(inner).join(fake).write('') self.args += ("-T", "regex:%%name:^.*%s/(?.*)" % outer) self.args += [str(tmpdir)] # Now, run the import and check that the imported object # is not in a container. > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:826: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:15:22,790 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:15:22,805 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:15:22,853 313 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:15:23,162 622 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:15:23,305 765 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 141ms. (143ms total) [0 unknowns] 2025-12-09 02:15:23,338 798 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:15:23,703 1163 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:15:23,905 1365 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:15:23,910 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:15:23,910 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:15:23,910 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:15:23,910 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:15:23,910 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:15:23,910 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:15:24,004 1464 [ main] INFO ome.formats.importer.ImportConfig - Using import target: regex:%name:^.*UniqueMultipleNameTemplateTargetArgument-Test-84fc8932-948b-4059-a1da-710eca7833f1/(?.*) 2025-12-09 02:15:24,034 1494 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:15:24,174 1634 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:15:24,184 1644 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testUniqueMultipleNameTemplate0/UniqueMultipleNameTemplateTargetArgument-Test-84fc8932-948b-4059-a1da-710eca7833f1/UniqueMultipleNameTemplateTargetArgument-Test-a771a999-4a52-4f37-824e-9ebf062fe183/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:15:24,194 1654 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testUniqueMultipleNameTemplate0/UniqueMultipleNameTemplateTargetArgument-Test-84fc8932-948b-4059-a1da-710eca7833f1/UniqueMultipleNameTemplateTargetArgument-Test-a771a999-4a52-4f37-824e-9ebf062fe183/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:15:24,204 1664 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testUniqueMultipleNameTemplate0/UniqueMultipleNameTemplateTargetArgument-Test-84fc8932-948b-4059-a1da-710eca7833f1/UniqueMultipleNameTemplateTargetArgument-Test-a771a999-4a52-4f37-824e-9ebf062fe183/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:15:24,227 1687 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:15:24,263 1723 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4036 2025-12-09 02:15:24,285 1745 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testUniqueMultipleNameTemplate0/UniqueMultipleNameTemplateTargetArgument-Test-84fc8932-948b-4059-a1da-710eca7833f1/UniqueMultipleNameTemplateTargetArgument-Test-a771a999-4a52-4f37-824e-9ebf062fe183/SPW&screens=0&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:15:24,293 1753 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:15:24,294 1754 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.294 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _______________ TestImport.testImportOutputDefaultWithScreen[1] ________________ self = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr0') capfd = <_pytest.capture.CaptureFixture object at 0x7f496ff55bd0>, plate = 1 @pytest.mark.parametrize("plate", [1, 2, 3]) def testImportOutputDefaultWithScreen(self, tmpdir, capfd, plate): """Test import summary argument with a screen""" fakefile = tmpdir.join("SPW&plates=%d&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake" % plate) fakefile.write('') self.args += [str(fakefile)] > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1010: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:16:32,633 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:16:32,649 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:16:32,698 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:16:33,008 628 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:16:33,152 772 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 142ms. (144ms total) [0 unknowns] 2025-12-09 02:16:33,185 805 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:16:33,542 1162 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:16:33,734 1354 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:16:33,739 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:16:33,739 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:16:33,739 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:16:33,739 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:16:33,739 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:16:33,739 1359 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:16:33,841 1461 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:16:33,980 1600 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:16:33,989 1609 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:16:33,999 1619 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:16:34,008 1628 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:16:34,032 1652 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:16:34,077 1697 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4111 2025-12-09 02:16:34,079 1699 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:16:34,082 1702 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:16:34,083 1703 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.248 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _______________ TestImport.testImportOutputDefaultWithScreen[2] ________________ self = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr1') capfd = <_pytest.capture.CaptureFixture object at 0x7f49843c9010>, plate = 2 @pytest.mark.parametrize("plate", [1, 2, 3]) def testImportOutputDefaultWithScreen(self, tmpdir, capfd, plate): """Test import summary argument with a screen""" fakefile = tmpdir.join("SPW&plates=%d&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake" % plate) fakefile.write('') self.args += [str(fakefile)] > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1010: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:16:35,004 257 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:16:35,019 272 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:16:35,069 322 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:16:35,380 633 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:16:35,523 776 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (142ms total) [0 unknowns] 2025-12-09 02:16:35,557 810 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:16:35,923 1176 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:16:36,148 1401 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:16:36,153 1406 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:16:36,153 1406 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:16:36,153 1406 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:16:36,153 1406 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:16:36,153 1406 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:16:36,153 1406 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:16:36,249 1502 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:16:36,400 1653 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:16:36,410 1663 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr1/SPW&plates=2&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:16:36,420 1673 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr1/SPW&plates=2&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:16:36,430 1683 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr1/SPW&plates=2&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:16:36,456 1709 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:16:36,501 1754 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4114 2025-12-09 02:16:36,505 1758 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr1/SPW&plates=2&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:16:36,508 1761 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:16:36,508 1761 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.267 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _______________ TestImport.testImportOutputDefaultWithScreen[3] ________________ self = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr2') capfd = <_pytest.capture.CaptureFixture object at 0x7f49841f2210>, plate = 3 @pytest.mark.parametrize("plate", [1, 2, 3]) def testImportOutputDefaultWithScreen(self, tmpdir, capfd, plate): """Test import summary argument with a screen""" fakefile = tmpdir.join("SPW&plates=%d&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake" % plate) fakefile.write('') self.args += [str(fakefile)] > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1010: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:16:37,142 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:16:37,157 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:16:37,205 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:16:37,510 610 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:16:37,651 751 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 139ms. (141ms total) [0 unknowns] 2025-12-09 02:16:37,684 784 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:16:38,039 1139 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:16:38,242 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:16:38,247 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:16:38,247 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:16:38,247 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:16:38,247 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:16:38,247 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:16:38,247 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:16:38,344 1444 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:16:38,487 1587 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:16:38,496 1596 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr2/SPW&plates=3&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:16:38,506 1606 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr2/SPW&plates=3&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:16:38,515 1615 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr2/SPW&plates=3&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:16:38,540 1640 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:16:38,595 1695 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4117 2025-12-09 02:16:38,598 1698 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testImportOutputDefaultWithScr2/SPW&plates=3&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:16:38,600 1700 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:16:38,601 1701 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.263 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ____________________ TestImport.testNamingArguments[Plate] _____________________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_0') capfd = <_pytest.capture.CaptureFixture object at 0x7f496fbcfa10> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:10,255 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:10,270 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:10,319 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:10,627 625 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:10,771 769 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 141ms. (144ms total) [0 unknowns] 2025-12-09 02:17:10,804 802 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:11,171 1169 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:11,381 1379 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:11,388 1386 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:11,388 1386 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:11,388 1386 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:11,388 1386 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:11,388 1386 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:11,388 1386 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:11,488 1486 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:11,629 1627 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:11,638 1636 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:11,648 1646 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:11,658 1656 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:11,681 1679 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:11,727 1725 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4165 2025-12-09 02:17:11,730 1728 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:11,733 1731 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:11,733 1731 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.251 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ___________________ TestImport.testNamingArguments[Plate-x] ____________________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_x_0') capfd = <_pytest.capture.CaptureFixture object at 0x7f4984591890> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:12,380 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:12,395 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:12,444 316 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:12,757 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:12,901 773 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 142ms. (145ms total) [0 unknowns] 2025-12-09 02:17:12,934 806 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:13,294 1166 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:13,493 1365 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:13,498 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:13,498 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:13,499 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:13,499 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:13,499 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:13,499 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:13,593 1465 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:13,738 1610 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:13,747 1619 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_x_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:13,757 1629 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_x_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:13,766 1638 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_x_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:13,791 1663 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:13,838 1710 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4168 2025-12-09 02:17:13,841 1713 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_x_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:13,844 1716 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:13,844 1716 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.257 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ______________ TestImport.testNamingArguments[Plate--description] ______________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__des0') capfd = <_pytest.capture.CaptureFixture object at 0x7f497886d350> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:14,493 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:14,508 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:14,556 316 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:14,866 626 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:15,009 769 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 141ms. (143ms total) [0 unknowns] 2025-12-09 02:17:15,042 802 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:15,400 1160 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:15,597 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:15,602 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:15,602 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:15,602 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:15,602 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:15,602 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:15,602 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:16,600 2360 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:16,744 2504 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:16,754 2514 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__des0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:16,764 2524 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__des0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:16,773 2533 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__des0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:16,797 2557 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:16,844 2604 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4171 2025-12-09 02:17:16,847 2607 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__des0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:16,850 2610 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:16,850 2610 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.257 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ___________ TestImport.testNamingArguments[Plate--plate_description] ___________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla0') capfd = <_pytest.capture.CaptureFixture object at 0x7f499f4fda90> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:17,494 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:17,510 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:17,559 314 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:17,862 617 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:18,001 756 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (139ms total) [0 unknowns] 2025-12-09 02:17:18,033 788 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:18,400 1155 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:18,627 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:18,637 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:18,637 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:18,638 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:18,638 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:18,638 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:18,638 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:18,737 1492 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:18,878 1633 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:18,888 1643 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:18,898 1653 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:18,907 1662 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:18,931 1686 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:18,975 1730 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4174 2025-12-09 02:17:18,977 1732 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:18,980 1735 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:18,981 1736 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ___________________ TestImport.testNamingArguments[Plate-n] ____________________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n_0') capfd = <_pytest.capture.CaptureFixture object at 0x7f4979f201d0> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:19,631 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:19,646 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:19,695 316 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:20,008 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:20,151 772 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 141ms. (143ms total) [0 unknowns] 2025-12-09 02:17:20,185 806 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:20,555 1176 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:20,757 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:20,762 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:20,762 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:20,762 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:20,762 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:20,762 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:20,762 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:20,858 1479 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:20,994 1615 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:21,003 1624 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:21,013 1634 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:21,021 1642 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:21,044 1665 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:21,089 1710 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4177 2025-12-09 02:17:21,092 1713 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:21,094 1715 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:21,094 1715 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.243 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted __________________ TestImport.testNamingArguments[Plate-n-x] ___________________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n_x_0') capfd = <_pytest.capture.CaptureFixture object at 0x7f4994b5aa10> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:21,979 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:21,994 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:22,043 316 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:22,351 624 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:22,495 768 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 142ms. (144ms total) [0 unknowns] 2025-12-09 02:17:22,528 801 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:22,888 1161 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:23,079 1352 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:23,084 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:23,084 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:23,084 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:23,084 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:23,084 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:23,084 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:23,184 1457 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:23,324 1597 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:23,334 1607 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n_x_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:23,343 1616 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n_x_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:23,353 1626 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n_x_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:23,378 1651 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:23,422 1695 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4180 2025-12-09 02:17:23,425 1698 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n_x_0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:23,428 1701 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:23,428 1701 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.251 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _____________ TestImport.testNamingArguments[Plate-n--description] _____________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n__d0') capfd = <_pytest.capture.CaptureFixture object at 0x7f49799a4650> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:24,078 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:24,093 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:24,143 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:24,455 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:24,600 774 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 142ms. (145ms total) [0 unknowns] 2025-12-09 02:17:24,633 807 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:24,995 1169 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:25,191 1365 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:25,196 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:25,196 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:25,196 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:25,196 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:25,196 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:25,196 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:25,294 1468 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:25,440 1614 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:25,450 1624 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n__d0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:25,461 1635 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n__d0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:25,470 1644 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n__d0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:25,494 1668 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:25,540 1714 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4183 2025-12-09 02:17:25,543 1717 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n__d0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:25,545 1719 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:25,546 1720 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.258 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted __________ TestImport.testNamingArguments[Plate-n--plate_description] __________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n__p0') capfd = <_pytest.capture.CaptureFixture object at 0x7f499448f7d0> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:26,191 247 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:26,207 263 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:26,255 311 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:26,564 620 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:26,704 760 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (140ms total) [0 unknowns] 2025-12-09 02:17:26,739 795 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:27,100 1156 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:27,312 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:27,316 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:27,316 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:27,316 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:27,316 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:27,316 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:27,316 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:27,412 1468 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:27,553 1609 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:27,562 1618 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n__p0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:27,572 1628 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n__p0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:27,580 1636 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n__p0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:27,603 1659 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:27,650 1706 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4186 2025-12-09 02:17:27,653 1709 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate_n__p0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:27,656 1712 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:27,656 1712 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _________________ TestImport.testNamingArguments[Plate--name] __________________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam0') capfd = <_pytest.capture.CaptureFixture object at 0x7f4994126650> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:28,291 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:28,305 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:28,353 303 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:28,657 607 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:28,796 746 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (139ms total) [0 unknowns] 2025-12-09 02:17:28,829 779 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:29,191 1141 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:29,394 1344 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:29,399 1349 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:29,399 1349 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:29,399 1349 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:29,399 1349 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:29,399 1349 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:29,399 1349 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:29,497 1447 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:29,634 1584 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:29,644 1594 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:29,654 1604 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:29,663 1613 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:29,687 1637 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:29,731 1681 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4189 2025-12-09 02:17:29,733 1683 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam0/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:29,736 1686 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:29,736 1686 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.246 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ________________ TestImport.testNamingArguments[Plate--name-x] _________________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam1') capfd = <_pytest.capture.CaptureFixture object at 0x7f4994fcfad0> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:30,589 254 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:30,605 270 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:30,654 319 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:30,964 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:31,108 773 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 141ms. (144ms total) [0 unknowns] 2025-12-09 02:17:31,141 806 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:31,502 1167 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:31,707 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:31,712 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:31,712 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:31,712 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:31,712 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:31,712 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:31,712 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:31,809 1474 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:31,951 1616 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:31,961 1626 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam1/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:31,970 1635 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam1/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:31,979 1644 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam1/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:32,003 1668 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:32,052 1717 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4192 2025-12-09 02:17:32,055 1720 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam1/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:32,058 1723 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:32,058 1723 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.256 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ___________ TestImport.testNamingArguments[Plate--name--description] ___________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam2') capfd = <_pytest.capture.CaptureFixture object at 0x7f497a5ea010> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:32,700 248 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:32,715 263 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:32,764 312 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:33,074 622 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:33,217 765 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 141ms. (143ms total) [0 unknowns] 2025-12-09 02:17:33,253 801 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:33,634 1182 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:33,835 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:33,839 1387 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:33,839 1387 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:33,839 1387 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:33,840 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:33,840 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:33,840 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:33,937 1485 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:34,082 1630 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:34,092 1640 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam2/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:34,101 1649 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam2/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:34,109 1657 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam2/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:34,133 1681 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:34,181 1729 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4195 2025-12-09 02:17:34,183 1731 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam2/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:34,186 1734 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:34,186 1734 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.256 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ________ TestImport.testNamingArguments[Plate--name--plate_description] ________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam3') capfd = <_pytest.capture.CaptureFixture object at 0x7f49935e4090> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:34,837 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:34,852 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:34,901 314 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:35,212 625 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:35,355 768 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 141ms. (143ms total) [0 unknowns] 2025-12-09 02:17:35,388 801 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:35,750 1163 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:35,952 1365 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:35,957 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:35,957 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:35,957 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:35,957 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:35,957 1370 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:35,958 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:36,056 1469 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:36,201 1614 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:36,211 1624 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam3/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:36,221 1634 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam3/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:36,230 1643 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam3/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:36,254 1667 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:36,302 1715 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4198 2025-12-09 02:17:36,305 1718 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__nam3/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:36,308 1721 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:36,308 1721 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.259 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ______________ TestImport.testNamingArguments[Plate--plate_name] _______________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla1') capfd = <_pytest.capture.CaptureFixture object at 0x7f4994aed1d0> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:36,948 251 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:36,963 266 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:37,012 315 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:37,324 627 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:37,467 770 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 139ms. (142ms total) [0 unknowns] 2025-12-09 02:17:37,499 802 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:37,860 1163 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:38,063 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:38,069 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:38,069 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:38,069 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:38,069 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:38,069 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:38,069 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:38,168 1471 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:38,309 1612 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:38,319 1622 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla1/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:38,328 1631 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla1/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:38,336 1639 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla1/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:38,360 1663 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:38,409 1712 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4201 2025-12-09 02:17:38,412 1715 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla1/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:38,415 1718 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:38,415 1718 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.254 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _____________ TestImport.testNamingArguments[Plate--plate_name-x] ______________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla2') capfd = <_pytest.capture.CaptureFixture object at 0x7f49943ecf50> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:39,072 254 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:39,088 270 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:39,137 319 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:39,452 634 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:39,597 779 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 143ms. (145ms total) [0 unknowns] 2025-12-09 02:17:39,630 812 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:39,996 1178 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:40,200 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:40,206 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:40,206 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:40,206 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:40,206 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:40,206 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:40,206 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:40,304 1486 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:40,444 1626 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:40,454 1636 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla2/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:40,464 1646 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla2/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:40,472 1654 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla2/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:40,496 1678 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:40,542 1724 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4204 2025-12-09 02:17:40,545 1727 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla2/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:40,547 1729 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:40,548 1730 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.249 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ________ TestImport.testNamingArguments[Plate--plate_name--description] ________ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla3') capfd = <_pytest.capture.CaptureFixture object at 0x7f4994bef8d0> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:41,369 248 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:41,384 263 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:41,432 311 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:41,741 620 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:41,882 761 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 139ms. (142ms total) [0 unknowns] 2025-12-09 02:17:41,915 794 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:42,273 1152 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:42,488 1367 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:42,494 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:42,494 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:42,494 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:42,494 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:42,494 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:42,494 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:42,587 1466 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:42,741 1620 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:42,751 1630 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla3/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:42,760 1639 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla3/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:42,769 1648 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla3/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:42,792 1671 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:42,837 1716 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4207 2025-12-09 02:17:42,840 1719 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla3/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:42,843 1722 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:42,843 1722 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.262 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _____ TestImport.testNamingArguments[Plate--plate_name--plate_description] _____ self = fixture = tmpdir = local('/tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla4') capfd = <_pytest.capture.CaptureFixture object at 0x7f497ab52150> @pytest.mark.parametrize("fixture", NFS, ids=NFS_names) def testNamingArguments(self, fixture, tmpdir, capfd): """Test naming arguments for the imported image/plate""" if fixture.obj_type == 'Image': fakefile = tmpdir.join("test.fake") else: fakefile = tmpdir.join("SPW&plates=1&plateRows=1&plateCols=1&" "fields=1&plateAcqs=1.fake") fakefile.write('') self.args += [str(fakefile)] if fixture.name_arg: self.args += [fixture.name_arg, 'name'] if fixture.description_arg: self.args += [fixture.description_arg, 'description'] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1111: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 02:17:43,473 243 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 02:17:43,488 258 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 02:17:43,536 306 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 02:17:43,838 608 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 02:17:43,977 747 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (139ms total) [0 unknowns] 2025-12-09 02:17:44,009 779 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 02:17:44,369 1139 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 02:17:44,566 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 02:17:44,577 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 02:17:44,577 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 02:17:44,577 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 02:17:44,577 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 02:17:44,577 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 02:17:44,577 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 02:17:44,676 1446 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION 2025-12-09 02:17:44,817 1587 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START 2025-12-09 02:17:44,828 1598 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla4/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake... 2025-12-09 02:17:44,838 1608 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla4/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:44,846 1616 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla4/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake 2025-12-09 02:17:44,870 1640 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END 2025-12-09 02:17:44,916 1686 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4210 2025-12-09 02:17:44,919 1689 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /tmp/pytest-of-omero/pytest-60/testNamingArguments_Plate__pla4/SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) java.lang.RuntimeException: Failure response on import! Category: ::omero::grid::ImportRequest Name: error-on-init Parameters: {stacktrace=java.lang.NullPointerException at ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296) at ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214) at ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498) at loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221) at loci.formats.in.FakeReader.initFile(FakeReader.java:984) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.formats.ImageReader.setId(ImageReader.java:864) at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelFiller.setId(ChannelFiller.java:258) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at loci.formats.Memoizer.setId(Memoizer.java:726) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692) at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412) at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763) at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245) at omero.cmd.HandleI.steps(HandleI.java:438) at omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509) at omero.cmd.HandleI$2.doWork(HandleI.java:383) at omero.cmd.HandleI$2.doWork(HandleI.java:380) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at omero.cmd.HandleI.run(HandleI.java:379) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at ome.services.util.Executor$Impl$1.call(Executor.java:488) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) , message=} at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807) at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118) at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:44,921 1691 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.Exception: Import failure at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2025-12-09 02:17:44,922 1692 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.252 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _____________________________ TestUser.testSaveAs ______________________________ self = gatewaywrapper = def testSaveAs(self, gatewaywrapper): for u in (gatewaywrapper.AUTHOR, gatewaywrapper.ADMIN): # Test image should be owned by author gatewaywrapper.loginAsAuthor() > image = gatewaywrapper.getTestImage(autocreate=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/gatewaytest/test_user.py:34: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/testdb_create.py:148: in getTestImage return dbhelpers.getImage(self.gateway, 'testimg1', forceds=dataset, ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:489: in getImage i = IMAGES[alias].create() ^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def create(self): if isinstance(self.dataset, str): dataset = DATASETS[self.dataset] project = PROJECTS[dataset.project] client = USERS[project.owner].login() dataset = dataset.get(client) else: dataset = self.dataset client = dataset._conn i = self.get(client, dataset) if i is not None: # print ".. -> image already exists: %s" % self.name return i # print ".. -> create new image: %s" % self.name sys.stderr.write('I') if self.filename is False: UserEntry.setGroupForSession( client, dataset.getDetails().getGroup().getName()) self._createWithoutPixels(client, dataset) return self.get(client, dataset) fpath = os.path.join(BASEPATH, self.filename) if not os.path.exists(fpath): if not os.path.exists(os.path.dirname(fpath)): os.makedirs(os.path.dirname(fpath)) if self.filename.endswith('.fake'): # If it's a .fake file, simply create it os.close(os.open(fpath, os.O_CREAT | os.O_EXCL)) else: raise IOError('No such file %s' % fpath) host = dataset._conn.c.ic.getProperties().getProperty( 'omero.host') or 'localhost' port = dataset._conn.c.ic.getProperties().getProperty( 'omero.port') or '4063' exe = "omero" newconn = dataset._conn.clone() newconn.connect() try: UserEntry.setGroupForSession( newconn, dataset.getDetails().getGroup().getName()) session = newconn._sessionUuid # print session exe += ' -s %s -k %s -p %s import -d %i --output legacy -n' % ( host, session, port, dataset.getId()) exe = exe.split() + [self.name, fpath] print(' '.join(exe)) try: p = subprocess.Popen( exe, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError: print("!!Please make sure the 'omero' executable is in PATH") return None pid = p.communicate() try: img = omero.gateway.ImageWrapper( dataset._conn, dataset._conn.getQueryService().find( > 'Pixels', int(pid[0].split(b'\n')[0].strip())).image) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E ValueError: invalid literal for int() with base 10: b'' ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/dbhelpers.py:442: ValueError ----------------------------- Captured stdout call ----------------------------- omero -s localhost -k ab96782f-c569-409a-a627-f849568766e4 -p 14064 import -d 1086 --output legacy -n weblitz_test_priv_image /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake (b'', b'Joined session for weblitz_test_author@localhost:14064. Idle timeout: 10 min. Current group: weblitz_test_author_group\n2025-12-09 02:43:21,348 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:43:21,364 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:43:21,412 313 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:43:21,413 314 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:43:21,721 622 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:43:21,862 763 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 139ms. (141ms total) [0 unknowns]\n2025-12-09 02:43:21,894 795 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:43:22,260 1161 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:43:22,462 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:43:22,467 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:43:22,467 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:43:22,467 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:43:22,467 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:43:22,467 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:43:22,467 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:43:22,810 1711 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1086\n2025-12-09 02:43:22,823 1724 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Import target specifies container: Dataset:1086\n2025-12-09 02:43:22,826 1727 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:43:22,994 1895 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:43:23,004 1905 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake...\n2025-12-09 02:43:23,017 1918 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:43:23,028 1929 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\n2025-12-09 02:43:23,033 1934 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini...\n2025-12-09 02:43:23,043 1944 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:43:23,053 1954 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake.ini\n2025-12-09 02:43:23,088 1989 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:43:23,131 2032 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4901\n2025-12-09 02:43:23,158 2059 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/scripts/imgs/testimg.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:43:23,161 2062 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:43:23,161 2062 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n2 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.590\n') ----------------------------- Captured stderr call ----------------------------- 2025-12-09 02:43:16,789 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) 2025-12-09 02:43:16,823 INFO [ omero.gateway] (MainThread) created connection (uuid=ee4df83e-de46-45bb-95cf-baddb14a9e89) 2025-12-09 02:43:16,892 INFO [ omero.gateway] (MainThread) created connection (uuid=ac9ddcb3-0c64-4c55-afc2-4204a8c2b659) I2025-12-09 02:43:16,954 INFO [ omero.gateway] (MainThread) created connection (uuid=ab96782f-c569-409a-a627-f849568766e4) 2025-12-09 02:43:23,309 INFO [ omero.gateway] (MainThread) closed connection (uuid=None) ------------------------------ Captured log call ------------------------------- INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=ee4df83e-de46-45bb-95cf-baddb14a9e89) INFO omero.gateway:__init__.py:2307 created connection (uuid=ac9ddcb3-0c64-4c55-afc2-4204a8c2b659) INFO omero.gateway:__init__.py:2307 created connection (uuid=ab96782f-c569-409a-a627-f849568766e4) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ________ TestPopulateMetadata.testPopulateMetadata[None-Screen2Plates] _________ self = fixture = batch_size = None @mark.parametrize("fixture", METADATA_FIXTURES, ids=METADATA_IDS) @mark.parametrize("batch_size", (None, 1, 10)) def testPopulateMetadata(self, fixture, batch_size): """ We should really test each of the parsing contexts in separate tests but in practice each one uses data created by the others, so for now just run them all together """ fixture.init(self) > t = self._test_parsing_context(fixture, batch_size) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1024: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:211: in get_target self.screen = self.createScreen(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:136: in createScreen plate1 = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ph6h8nxm&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '13ded21a-bbf1-454f-82f5-7627467b5007' args = ['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', ...] popen = out = b'' err = b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d26...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.259\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ph6h8nxm&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:05,235 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:05,250 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:05,297 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:05,298 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:05,298 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:05,298 304 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:05,298 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:05,298 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:05,598 604 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:05,737 743 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (139ms total) [0 unknowns]\n2025-12-09 02:44:05,769 775 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:06,161 1167 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:06,357 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:06,362 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:06,362 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:06,362 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:06,362 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:06,362 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:06,362 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:06,424 1430 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:06,568 1574 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:06,575 1581 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ph6h8nxm&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:44:06,586 1592 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ph6h8nxm&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:06,595 1601 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ph6h8nxm&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:06,621 1627 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:06,667 1673 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4926\n2025-12-09 02:44:06,675 1681 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ph6h8nxm&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:06,678 1684 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:06,678 1684 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.259\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _________ TestPopulateMetadata.testPopulateMetadata[None-Plate2Wells] __________ self = fixture = batch_size = None @mark.parametrize("fixture", METADATA_FIXTURES, ids=METADATA_IDS) @mark.parametrize("batch_size", (None, 1, 10)) def testPopulateMetadata(self, fixture, batch_size): """ We should really test each of the parsing contexts in separate tests but in practice each one uses data created by the others, so for now just run them all together """ fixture.init(self) > t = self._test_parsing_context(fixture, batch_size) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1024: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_076rz4ikh&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '13ded21a-bbf1-454f-82f5-7627467b5007' args = ['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', ...] popen = out = b'' err = b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d26...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.245\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_076rz4ikh&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:08,219 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:08,234 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:08,281 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:08,282 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:08,282 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:08,282 304 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:08,283 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:08,283 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:08,582 604 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:08,721 743 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (139ms total) [0 unknowns]\n2025-12-09 02:44:08,753 775 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:09,110 1132 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:09,312 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:09,317 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:09,317 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:09,317 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:09,317 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:09,317 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:09,317 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:09,380 1402 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:09,516 1538 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:09,522 1544 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_076rz4ikh&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:44:09,533 1555 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_076rz4ikh&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:09,541 1563 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_076rz4ikh&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:09,567 1589 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:09,610 1632 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4929\n2025-12-09 02:44:09,617 1639 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_076rz4ikh&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:09,620 1642 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:09,620 1642 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.245\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception __________ TestPopulateMetadata.testPopulateMetadata[1-Screen2Plates] __________ self = fixture = , batch_size = 1 @mark.parametrize("fixture", METADATA_FIXTURES, ids=METADATA_IDS) @mark.parametrize("batch_size", (None, 1, 10)) def testPopulateMetadata(self, fixture, batch_size): """ We should really test each of the parsing contexts in separate tests but in practice each one uses data created by the others, so for now just run them all together """ fixture.init(self) > t = self._test_parsing_context(fixture, batch_size) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1024: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:211: in get_target self.screen = self.createScreen(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:136: in createScreen plate1 = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_02tc7yfco&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '13ded21a-bbf1-454f-82f5-7627467b5007' args = ['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', ...] popen = out = b'' err = b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d26...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.260\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_02tc7yfco&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:36,629 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:36,644 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:36,691 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:36,692 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:36,692 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:36,692 304 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:36,692 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:36,692 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:37,005 617 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:37,151 763 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 144ms. (146ms total) [0 unknowns]\n2025-12-09 02:44:37,186 798 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:37,559 1171 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:37,771 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:37,776 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:37,777 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:37,777 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:37,777 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:37,777 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:37,777 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:37,841 1453 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:37,991 1603 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:37,998 1610 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_02tc7yfco&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:44:38,010 1622 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_02tc7yfco&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:38,019 1631 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_02tc7yfco&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:38,044 1656 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:38,090 1702 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4955\n2025-12-09 02:44:38,093 1705 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_02tc7yfco&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:38,095 1707 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:38,096 1708 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.260\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception ___________ TestPopulateMetadata.testPopulateMetadata[1-Plate2Wells] ___________ self = fixture = , batch_size = 1 @mark.parametrize("fixture", METADATA_FIXTURES, ids=METADATA_IDS) @mark.parametrize("batch_size", (None, 1, 10)) def testPopulateMetadata(self, fixture, batch_size): """ We should really test each of the parsing contexts in separate tests but in practice each one uses data created by the others, so for now just run them all together """ fixture.init(self) > t = self._test_parsing_context(fixture, batch_size) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1024: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0r_0f_nyz&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '13ded21a-bbf1-454f-82f5-7627467b5007' args = ['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', ...] popen = out = b'' err = b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d26...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.292\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0r_0f_nyz&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:39,661 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:39,676 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:39,723 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:39,724 305 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:39,724 305 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:39,724 305 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:39,724 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:39,724 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:40,025 606 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:40,165 746 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (140ms total) [0 unknowns]\n2025-12-09 02:44:40,197 778 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:40,547 1128 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:40,743 1324 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:40,748 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:40,748 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:40,748 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:40,748 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:40,748 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:40,748 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:40,817 1398 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:40,992 1573 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:40,998 1579 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0r_0f_nyz&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:44:41,010 1591 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0r_0f_nyz&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:41,019 1600 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0r_0f_nyz&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:41,051 1632 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:41,095 1676 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4958\n2025-12-09 02:44:41,101 1682 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0r_0f_nyz&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:41,104 1685 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:41,104 1685 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.292\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _________ TestPopulateMetadata.testPopulateMetadata[10-Screen2Plates] __________ self = fixture = batch_size = 10 @mark.parametrize("fixture", METADATA_FIXTURES, ids=METADATA_IDS) @mark.parametrize("batch_size", (None, 1, 10)) def testPopulateMetadata(self, fixture, batch_size): """ We should really test each of the parsing contexts in separate tests but in practice each one uses data created by the others, so for now just run them all together """ fixture.init(self) > t = self._test_parsing_context(fixture, batch_size) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1024: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:211: in get_target self.screen = self.createScreen(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:136: in createScreen plate1 = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0sl62cvm4&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '13ded21a-bbf1-454f-82f5-7627467b5007' args = ['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', ...] popen = out = b'' err = b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d26...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.241\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0sl62cvm4&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:48,431 244 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:48,448 261 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:48,497 310 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:48,497 310 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:48,498 311 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:48,498 311 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:48,498 311 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:48,498 311 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:48,803 616 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:48,945 758 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (142ms total) [0 unknowns]\n2025-12-09 02:44:48,978 791 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:49,343 1156 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:49,545 1358 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:49,556 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:49,556 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:49,556 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:49,556 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:49,556 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:49,556 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:49,622 1435 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:49,755 1568 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:49,762 1575 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0sl62cvm4&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:44:49,772 1585 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0sl62cvm4&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:49,781 1594 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0sl62cvm4&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:49,805 1618 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:49,852 1665 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4966\n2025-12-09 02:44:49,855 1668 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0sl62cvm4&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:49,858 1671 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:49,858 1671 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.241\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception __________ TestPopulateMetadata.testPopulateMetadata[10-Plate2Wells] ___________ self = fixture = , batch_size = 10 @mark.parametrize("fixture", METADATA_FIXTURES, ids=METADATA_IDS) @mark.parametrize("batch_size", (None, 1, 10)) def testPopulateMetadata(self, fixture, batch_size): """ We should really test each of the parsing contexts in separate tests but in practice each one uses data created by the others, so for now just run them all together """ fixture.init(self) > t = self._test_parsing_context(fixture, batch_size) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1024: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_048tz9q5r&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '13ded21a-bbf1-454f-82f5-7627467b5007' args = ['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', ...] popen = out = b'' err = b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d26...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.262\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_048tz9q5r&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:51,431 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:51,447 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:51,495 313 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:51,496 314 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:51,496 314 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:51,496 314 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:51,496 314 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:51,496 314 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:51,804 622 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:51,946 764 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (143ms total) [0 unknowns]\n2025-12-09 02:44:51,979 797 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:52,339 1157 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:52,540 1358 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:52,545 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:52,546 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:52,546 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:52,546 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:52,546 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:52,546 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:52,610 1428 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:52,758 1576 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:52,765 1583 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_048tz9q5r&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:44:52,776 1594 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_048tz9q5r&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:52,785 1603 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_048tz9q5r&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:52,810 1628 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:52,857 1675 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4969\n2025-12-09 02:44:52,863 1681 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_048tz9q5r&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:52,866 1684 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:52,867 1685 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.262\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception ________ TestPopulateMetadata.testPopulateMetadataNsAnns[Plate2WellsNs] ________ self = fixture = @mark.parametrize("fixture", METADATA_NS_FIXTURES, ids=METADATA_NS_IDS) def testPopulateMetadataNsAnns(self, fixture): """ Test complicated annotations (multiple ns/groups) on a single OMERO data type, as opposed to testPopulateMetadata which tests simple annotations on multiple OMERO data types """ fixture.init(self) > t = self._test_parsing_context(fixture, 2) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1037: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0v46p221w&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 4, 'plateRows': 2, ...} server = 'localhost', port = '14064' key = '13ded21a-bbf1-454f-82f5-7627467b5007' args = ['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', ...] popen = out = b'' err = b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d26...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.274\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0v46p221w&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 E b'' E b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:57,869 247 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:57,884 262 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:57,933 311 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:57,934 312 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:57,934 312 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:57,934 312 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:57,934 312 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:57,934 312 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:58,241 619 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:58,388 766 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 144ms. (147ms total) [0 unknowns]\n2025-12-09 02:44:58,421 799 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:58,770 1148 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:58,971 1349 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:58,977 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:58,977 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:58,977 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:58,977 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:58,977 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:58,977 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:59,040 1418 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:59,195 1573 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:59,202 1580 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0v46p221w&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:44:59,214 1592 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0v46p221w&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:44:59,224 1602 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0v46p221w&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:44:59,256 1634 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:59,302 1680 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4977\n2025-12-09 02:44:59,306 1684 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0v46p221w&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:59,308 1686 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:59,309 1687 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.274\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _______ TestPopulateMetadata.testPopulateMetadataNsAnns[Plate2WellsNs2] ________ self = fixture = @mark.parametrize("fixture", METADATA_NS_FIXTURES, ids=METADATA_NS_IDS) def testPopulateMetadataNsAnns(self, fixture): """ Test complicated annotations (multiple ns/groups) on a single OMERO data type, as opposed to testPopulateMetadata which tests simple annotations on multiple OMERO data types """ fixture.init(self) > t = self._test_parsing_context(fixture, 2) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1037: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_04jmzhh03&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 4, 'plateRows': 2, ...} server = 'localhost', port = '14064' key = '13ded21a-bbf1-454f-82f5-7627467b5007' args = ['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', ...] popen = out = b'' err = b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d26...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.265\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_04jmzhh03&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 E b'' E b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:45:00,885 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:00,900 264 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:00,948 312 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:00,949 313 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:00,949 313 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:00,949 313 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:00,949 313 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:00,949 313 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:01,259 623 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:01,405 769 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 144ms. (146ms total) [0 unknowns]\n2025-12-09 02:45:01,438 802 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:01,799 1163 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:02,005 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:02,010 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:02,010 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:02,010 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:02,010 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:02,010 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:02,010 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:02,080 1444 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:02,231 1595 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:02,238 1602 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_04jmzhh03&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:02,250 1614 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_04jmzhh03&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:02,259 1623 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_04jmzhh03&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:02,283 1647 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:02,331 1695 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4980\n2025-12-09 02:45:02,337 1701 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_04jmzhh03&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:02,340 1704 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:02,340 1704 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.265\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _______ TestPopulateMetadata.testPopulateMetadataNsAnnsUnavailableHeader _______ self = def testPopulateMetadataNsAnnsUnavailableHeader(self): """ Similar to testPopulateMetadataNsAnns but use two plates and check MapAnnotations aren't duplicated """ fixture_empty = Plate2WellsNs2UnavailableHeader() fixture_empty.init(self) > self._test_parsing_context(fixture_empty, 2) test/integration/metadata/test_populate.py:1058: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0i7c31p6_&&plates=1&plateAcqs=1&plateCols=2&plateRows=2&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 2, ...} server = 'localhost', port = '14064' key = '13ded21a-bbf1-454f-82f5-7627467b5007' args = ['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', ...] popen = out = b'' err = b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d26...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.248\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0i7c31p6_&&plates=1&plateAcqs=1&plateCols=2&plateRows=2&fields=1.fake')]] 2 E b'' E b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:45:03,899 240 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:03,914 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:03,963 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:03,963 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:03,964 305 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:03,964 305 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:03,964 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:03,964 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:04,264 605 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:04,404 745 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (140ms total) [0 unknowns]\n2025-12-09 02:45:04,436 777 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:04,790 1131 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:04,980 1321 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:04,984 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:04,985 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:04,985 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:04,985 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:04,985 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:04,985 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:05,052 1393 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:05,189 1530 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:05,196 1537 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0i7c31p6_&&plates=1&plateAcqs=1&plateCols=2&plateRows=2&fields=1.fake...\n2025-12-09 02:45:05,206 1547 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0i7c31p6_&&plates=1&plateAcqs=1&plateCols=2&plateRows=2&fields=1.fake\n2025-12-09 02:45:05,217 1558 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0i7c31p6_&&plates=1&plateAcqs=1&plateCols=2&plateRows=2&fields=1.fake\n2025-12-09 02:45:05,242 1583 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:05,289 1630 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4983\n2025-12-09 02:45:05,293 1634 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0i7c31p6_&&plates=1&plateAcqs=1&plateCols=2&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:05,295 1636 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:05,296 1637 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.248\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _____________ TestPopulateMetadata.testPopulateMetadataNsAnnsFail ______________ self = def testPopulateMetadataNsAnnsFail(self): """ Similar to testPopulateMetadataNsAnns but use two plates and check MapAnnotations aren't duplicated """ fixture_fail = Plate2WellsNs2Fail() fixture_fail.init(self) > self._test_parsing_context(fixture_fail, 2) test/integration/metadata/test_populate.py:1068: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_00jtdq09t&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '13ded21a-bbf1-454f-82f5-7627467b5007' args = ['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', ...] popen = out = b'' err = b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d26...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.247\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_00jtdq09t&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:45:06,854 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:06,870 266 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:06,918 314 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:06,919 315 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:06,920 316 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:06,920 316 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:06,920 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:06,920 316 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:07,229 625 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:07,373 769 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 142ms. (144ms total) [0 unknowns]\n2025-12-09 02:45:07,406 802 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:07,764 1160 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:07,971 1367 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:07,976 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:07,976 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:07,976 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:07,976 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:07,976 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:07,976 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:08,041 1437 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:08,177 1573 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:08,184 1580 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_00jtdq09t&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:45:08,195 1591 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_00jtdq09t&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:08,204 1600 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_00jtdq09t&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:08,229 1625 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:08,276 1672 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4986\n2025-12-09 02:45:08,280 1676 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_00jtdq09t&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:08,283 1679 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:08,283 1679 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.247\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _______ TestPopulateMetadataDedup.testPopulateMetadataNsAnnsDedup[None] ________ self = ns = None @mark.parametrize("ns", [None, NSBULKANNOTATIONS, MAPR_NS_GENE]) def testPopulateMetadataNsAnnsDedup(self, ns): """ Similar to testPopulateMetadataNsAnns but use two plates, check MapAnnotations aren't duplicated, and filter by namespace """ fixture1 = Plate2WellsNs2() fixture1.init(self) > self._test_parsing_context(fixture1, 2) test/integration/metadata/test_populate.py:1199: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0k10bqkuc&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 4, 'plateRows': 2, ...} server = 'localhost', port = '14064' key = '3a8ef545-99b6-4cca-af45-f2cc0dfaa304' args = ['omero', '-s', 'localhost', '-k', '3a8ef545-99b6-4cca-af45-f2cc0dfaa304', '-p', ...] popen = out = b'' err = b'Joined session for 30ddef33-19ad-48c2-b930-80249024ea58@localhost:14064. Idle timeout: 10 min. Current group: 0dc162...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.254\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '3a8ef545-99b6-4cca-af45-f2cc0dfaa304', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0k10bqkuc&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 E b'' E b'Joined session for 30ddef33-19ad-48c2-b930-80249024ea58@localhost:14064. Idle timeout: 10 min. Current group: 0dc1629f-b52b-415a-aa24-b48de9cb4b9a\n2025-12-09 02:45:12,157 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:12,172 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:12,221 314 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:12,222 315 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:12,222 315 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:12,222 315 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:12,222 315 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:12,223 316 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:12,535 628 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:12,682 775 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 145ms. (148ms total) [0 unknowns]\n2025-12-09 02:45:12,715 808 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:13,070 1163 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:13,265 1358 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:13,275 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:13,275 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:13,275 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:13,275 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:13,275 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:13,275 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:13,340 1433 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:13,483 1576 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:13,489 1582 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0k10bqkuc&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:13,499 1592 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0k10bqkuc&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:13,508 1601 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0k10bqkuc&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:13,532 1625 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:13,578 1671 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4992\n2025-12-09 02:45:13,586 1679 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0k10bqkuc&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:13,589 1682 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:13,589 1682 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.254\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _ TestPopulateMetadataDedup.testPopulateMetadataNsAnnsDedup[openmicroscopy.org/omero/bulk_annotations] _ self = ns = 'openmicroscopy.org/omero/bulk_annotations' @mark.parametrize("ns", [None, NSBULKANNOTATIONS, MAPR_NS_GENE]) def testPopulateMetadataNsAnnsDedup(self, ns): """ Similar to testPopulateMetadataNsAnns but use two plates, check MapAnnotations aren't duplicated, and filter by namespace """ fixture1 = Plate2WellsNs2() fixture1.init(self) > self._test_parsing_context(fixture1, 2) test/integration/metadata/test_populate.py:1199: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09o9xsynh&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 4, 'plateRows': 2, ...} server = 'localhost', port = '14064' key = 'e41045b2-76e8-47ef-9546-b92781542fb7' args = ['omero', '-s', 'localhost', '-k', 'e41045b2-76e8-47ef-9546-b92781542fb7', '-p', ...] popen = out = b'' err = b'Joined session for aa934116-76dd-492a-95fa-44044c3670e5@localhost:14064. Idle timeout: 10 min. Current group: c4ba8c...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.271\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'e41045b2-76e8-47ef-9546-b92781542fb7', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09o9xsynh&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 E b'' E b'Joined session for aa934116-76dd-492a-95fa-44044c3670e5@localhost:14064. Idle timeout: 10 min. Current group: c4ba8cba-9dcf-42e7-bc8d-3ea57739afb4\n2025-12-09 02:45:17,059 254 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:17,075 270 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:17,125 320 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:17,126 321 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:17,126 321 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:17,126 321 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:17,126 321 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:17,126 321 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:17,438 633 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:17,586 781 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 145ms. (147ms total) [0 unknowns]\n2025-12-09 02:45:17,619 814 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:17,986 1181 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:18,189 1384 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:18,195 1390 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:18,195 1390 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:18,195 1390 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:18,195 1390 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:18,195 1390 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:18,195 1390 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:18,259 1454 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:18,415 1610 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:18,422 1617 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09o9xsynh&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:18,434 1629 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09o9xsynh&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:18,444 1639 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09o9xsynh&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:18,470 1665 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:18,516 1711 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4998\n2025-12-09 02:45:18,522 1717 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09o9xsynh&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:18,525 1720 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:18,525 1720 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.271\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _ TestPopulateMetadataDedup.testPopulateMetadataNsAnnsDedup[openmicroscopy.org/mapr/gene] _ self = ns = 'openmicroscopy.org/mapr/gene' @mark.parametrize("ns", [None, NSBULKANNOTATIONS, MAPR_NS_GENE]) def testPopulateMetadataNsAnnsDedup(self, ns): """ Similar to testPopulateMetadataNsAnns but use two plates, check MapAnnotations aren't duplicated, and filter by namespace """ fixture1 = Plate2WellsNs2() fixture1.init(self) > self._test_parsing_context(fixture1, 2) test/integration/metadata/test_populate.py:1199: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0mv9kpgka&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 4, 'plateRows': 2, ...} server = 'localhost', port = '14064' key = 'da5d3db1-b278-4026-af58-2ca45b4ee5aa' args = ['omero', '-s', 'localhost', '-k', 'da5d3db1-b278-4026-af58-2ca45b4ee5aa', '-p', ...] popen = out = b'' err = b'Joined session for 6e715598-2f14-4765-9e6e-511c8f2f3158@localhost:14064. Idle timeout: 10 min. Current group: 789ae2...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.254\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'da5d3db1-b278-4026-af58-2ca45b4ee5aa', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0mv9kpgka&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 E b'' E b'Joined session for 6e715598-2f14-4765-9e6e-511c8f2f3158@localhost:14064. Idle timeout: 10 min. Current group: 789ae208-8cdb-4356-947a-1fbc69da502b\n2025-12-09 02:45:22,642 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:22,658 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:22,707 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:22,708 319 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:22,708 319 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:22,708 319 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:22,708 319 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:22,708 319 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:23,018 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:23,167 778 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 146ms. (148ms total) [0 unknowns]\n2025-12-09 02:45:23,200 811 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:23,566 1177 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:23,775 1386 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:23,780 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:23,780 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:23,780 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:23,780 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:23,780 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:23,780 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:23,845 1456 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:23,986 1597 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:23,994 1605 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0mv9kpgka&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:24,005 1616 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0mv9kpgka&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:24,015 1626 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0mv9kpgka&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:24,040 1651 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:24,085 1696 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5004\n2025-12-09 02:45:24,091 1702 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0mv9kpgka&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:24,094 1705 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:24,094 1705 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.254\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception ____ TestPopulateMetadataDedup.testPopulateMetadataNsAnnsDedupDelete[None] _____ self = ns = None @mark.parametrize("ns", [None, NSBULKANNOTATIONS, MAPR_NS_GENE]) def testPopulateMetadataNsAnnsDedupDelete(self, ns): """ Similar to testPopulateMetadataNsAnns but use two plates, check MapAnnotations aren't duplicated, and delete by namespace """ fixture1 = Plate2WellsNs2() fixture1.init(self) > self._test_parsing_context(fixture1, 2) test/integration/metadata/test_populate.py:1215: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0f2se96od&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 4, 'plateRows': 2, ...} server = 'localhost', port = '14064' key = 'ea377c36-4ed2-4eb5-9e61-74b7ecec841d' args = ['omero', '-s', 'localhost', '-k', 'ea377c36-4ed2-4eb5-9e61-74b7ecec841d', '-p', ...] popen = out = b'' err = b'Joined session for d72dc75c-40d1-4813-a5d3-1cb4580108d5@localhost:14064. Idle timeout: 10 min. Current group: 5e1a75...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.253\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'ea377c36-4ed2-4eb5-9e61-74b7ecec841d', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0f2se96od&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 E b'' E b'Joined session for d72dc75c-40d1-4813-a5d3-1cb4580108d5@localhost:14064. Idle timeout: 10 min. Current group: 5e1a75b6-55e9-4267-bcbe-9ecb3e00cd8d\n2025-12-09 02:45:27,602 240 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:27,617 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:27,664 302 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:27,665 303 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:27,665 303 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:27,665 303 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:27,665 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:27,665 303 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:27,965 603 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:28,107 745 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (143ms total) [0 unknowns]\n2025-12-09 02:45:28,140 778 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:28,489 1127 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:28,683 1321 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:28,687 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:28,687 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:28,687 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:28,687 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:28,687 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:28,687 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:28,756 1394 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:28,896 1534 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:28,903 1541 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0f2se96od&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:28,914 1552 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0f2se96od&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:28,924 1562 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0f2se96od&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:28,949 1587 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:28,993 1631 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5010\n2025-12-09 02:45:29,000 1638 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0f2se96od&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:29,003 1641 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:29,004 1642 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.253\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _ TestPopulateMetadataDedup.testPopulateMetadataNsAnnsDedupDelete[openmicroscopy.org/omero/bulk_annotations] _ self = ns = 'openmicroscopy.org/omero/bulk_annotations' @mark.parametrize("ns", [None, NSBULKANNOTATIONS, MAPR_NS_GENE]) def testPopulateMetadataNsAnnsDedupDelete(self, ns): """ Similar to testPopulateMetadataNsAnns but use two plates, check MapAnnotations aren't duplicated, and delete by namespace """ fixture1 = Plate2WellsNs2() fixture1.init(self) > self._test_parsing_context(fixture1, 2) test/integration/metadata/test_populate.py:1215: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0reqs0fco&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 4, 'plateRows': 2, ...} server = 'localhost', port = '14064' key = '3f0c1530-1d7d-42f8-aa43-16f5a5b0bcf6' args = ['omero', '-s', 'localhost', '-k', '3f0c1530-1d7d-42f8-aa43-16f5a5b0bcf6', '-p', ...] popen = out = b'' err = b'Joined session for e5b46dd1-505c-452f-addd-d23a99fc6b54@localhost:14064. Idle timeout: 10 min. Current group: ea5c7e...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.260\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '3f0c1530-1d7d-42f8-aa43-16f5a5b0bcf6', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0reqs0fco&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 E b'' E b'Joined session for e5b46dd1-505c-452f-addd-d23a99fc6b54@localhost:14064. Idle timeout: 10 min. Current group: ea5c7eff-3b4b-4c15-910b-c5368a72084e\n2025-12-09 02:45:33,039 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:33,054 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:33,103 317 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:33,104 318 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:33,104 318 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:33,104 318 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:33,104 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:33,104 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:33,415 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:33,563 777 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 145ms. (148ms total) [0 unknowns]\n2025-12-09 02:45:33,596 810 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:33,956 1170 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:34,155 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:34,160 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:34,160 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:34,160 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:34,160 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:34,160 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:34,160 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:34,231 1445 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:34,374 1588 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:34,381 1595 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0reqs0fco&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:34,392 1606 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0reqs0fco&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:34,403 1617 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0reqs0fco&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:34,428 1642 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:34,474 1688 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5016\n2025-12-09 02:45:34,483 1697 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0reqs0fco&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:34,485 1699 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:34,486 1700 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.260\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _ TestPopulateMetadataDedup.testPopulateMetadataNsAnnsDedupDelete[openmicroscopy.org/mapr/gene] _ self = ns = 'openmicroscopy.org/mapr/gene' @mark.parametrize("ns", [None, NSBULKANNOTATIONS, MAPR_NS_GENE]) def testPopulateMetadataNsAnnsDedupDelete(self, ns): """ Similar to testPopulateMetadataNsAnns but use two plates, check MapAnnotations aren't duplicated, and delete by namespace """ fixture1 = Plate2WellsNs2() fixture1.init(self) > self._test_parsing_context(fixture1, 2) test/integration/metadata/test_populate.py:1215: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:894: in _test_parsing_context target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0b_u563ji&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 4, 'plateRows': 2, ...} server = 'localhost', port = '14064' key = 'c7d8d047-cd0b-4360-a6f6-60a2f110ca4e' args = ['omero', '-s', 'localhost', '-k', 'c7d8d047-cd0b-4360-a6f6-60a2f110ca4e', '-p', ...] popen = out = b'' err = b'Joined session for c9d80c0c-eff8-4d52-8673-c951237cbf9f@localhost:14064. Idle timeout: 10 min. Current group: b559e5...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'c7d8d047-cd0b-4360-a6f6-60a2f110ca4e', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0b_u563ji&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 E b'' E b'Joined session for c9d80c0c-eff8-4d52-8673-c951237cbf9f@localhost:14064. Idle timeout: 10 min. Current group: b559e526-0796-4719-af16-2a027d1705d2\n2025-12-09 02:45:37,891 288 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:37,907 304 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:37,956 353 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:37,957 354 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:37,957 354 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:37,957 354 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:37,957 354 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:37,957 354 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:38,270 667 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:38,420 817 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 148ms. (150ms total) [0 unknowns]\n2025-12-09 02:45:38,456 853 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:38,831 1228 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:39,041 1438 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:39,046 1443 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:39,047 1444 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:39,047 1444 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:39,047 1444 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:39,047 1444 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:39,047 1444 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:39,112 1509 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:39,250 1647 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:39,257 1654 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0b_u563ji&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:39,269 1666 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0b_u563ji&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:39,278 1675 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0b_u563ji&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:39,303 1700 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:39,350 1747 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5022\n2025-12-09 02:45:39,353 1750 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0b_u563ji&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:39,356 1753 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:39,356 1753 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception ________ TestPopulateMetadataConfigFiles.test_delete_attach[True-None] _________ self = ns = None, attach = True @mark.parametrize("ns", [None, NSBULKANNOTATIONS, NSBULKANNOTATIONSCONFIG]) @mark.parametrize("attach", [True, False]) def test_delete_attach(self, ns, attach): > fixture = self._init_fixture_attach_cfg() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1256: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:1231: in _init_fixture_attach_cfg target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09tyx960k&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = 'e7b5f762-b3ed-4e47-b0e8-934c8424014a' args = ['omero', '-s', 'localhost', '-k', 'e7b5f762-b3ed-4e47-b0e8-934c8424014a', '-p', ...] popen = out = b'' err = b'Joined session for c45563c1-d7f3-4a67-8c1a-20944565052c@localhost:14064. Idle timeout: 10 min. Current group: fa8618...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.246\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'e7b5f762-b3ed-4e47-b0e8-934c8424014a', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09tyx960k&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for c45563c1-d7f3-4a67-8c1a-20944565052c@localhost:14064. Idle timeout: 10 min. Current group: fa861828-ce40-4006-bb17-ee602134a2f7\n2025-12-09 02:45:43,393 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:43,409 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:43,457 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:43,458 317 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:43,458 317 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:43,458 317 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:43,459 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:43,459 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:43,770 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:43,913 772 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 141ms. (143ms total) [0 unknowns]\n2025-12-09 02:45:43,946 805 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:44,315 1174 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:44,518 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:44,522 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:44,522 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:44,522 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:44,522 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:44,522 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:44,523 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:44,584 1443 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:44,723 1582 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:44,730 1589 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09tyx960k&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:45:44,740 1599 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09tyx960k&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:44,750 1609 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09tyx960k&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:44,773 1632 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:44,817 1676 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5028\n2025-12-09 02:45:44,823 1682 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09tyx960k&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:44,826 1685 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:44,826 1685 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.246\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _ TestPopulateMetadataConfigFiles.test_delete_attach[True-openmicroscopy.org/omero/bulk_annotations] _ self = ns = 'openmicroscopy.org/omero/bulk_annotations', attach = True @mark.parametrize("ns", [None, NSBULKANNOTATIONS, NSBULKANNOTATIONSCONFIG]) @mark.parametrize("attach", [True, False]) def test_delete_attach(self, ns, attach): > fixture = self._init_fixture_attach_cfg() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1256: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:1231: in _init_fixture_attach_cfg target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_01wwkwsq9&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = 'd502e2d2-ebdf-4332-a089-72798e1c63f2' args = ['omero', '-s', 'localhost', '-k', 'd502e2d2-ebdf-4332-a089-72798e1c63f2', '-p', ...] popen = out = b'' err = b'Joined session for 81243c9b-054c-49d1-bd53-2bf76ce3fb5e@localhost:14064. Idle timeout: 10 min. Current group: ea97bf...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.270\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'd502e2d2-ebdf-4332-a089-72798e1c63f2', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_01wwkwsq9&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for 81243c9b-054c-49d1-bd53-2bf76ce3fb5e@localhost:14064. Idle timeout: 10 min. Current group: ea97bf3e-c06e-48e3-853d-04064c37de69\n2025-12-09 02:45:48,712 256 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:48,727 271 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:48,777 321 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:48,778 322 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:48,778 322 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:48,778 322 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:48,778 322 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:48,778 322 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:49,088 632 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:49,232 776 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 142ms. (143ms total) [0 unknowns]\n2025-12-09 02:45:49,265 809 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:49,632 1176 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:49,834 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:49,839 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:49,839 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:49,839 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:49,839 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:49,839 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:49,839 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:49,902 1446 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:50,063 1607 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:50,070 1614 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_01wwkwsq9&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:45:50,080 1624 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_01wwkwsq9&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:50,089 1633 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_01wwkwsq9&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:50,114 1658 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:50,159 1703 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5034\n2025-12-09 02:45:50,163 1707 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_01wwkwsq9&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:50,166 1710 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:50,167 1711 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.270\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _ TestPopulateMetadataConfigFiles.test_delete_attach[True-openmicroscopy.org/omero/bulk_annotations/config] _ self = ns = 'openmicroscopy.org/omero/bulk_annotations/config', attach = True @mark.parametrize("ns", [None, NSBULKANNOTATIONS, NSBULKANNOTATIONSCONFIG]) @mark.parametrize("attach", [True, False]) def test_delete_attach(self, ns, attach): > fixture = self._init_fixture_attach_cfg() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1256: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:1231: in _init_fixture_attach_cfg target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_0cvh5ds&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '3b96e06c-01b5-403d-abcb-5ecd8307accd' args = ['omero', '-s', 'localhost', '-k', '3b96e06c-01b5-403d-abcb-5ecd8307accd', '-p', ...] popen = out = b'' err = b'Joined session for 10c7a71b-7e26-4c0e-b64c-452b66b19f3a@localhost:14064. Idle timeout: 10 min. Current group: 14e4cf...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '3b96e06c-01b5-403d-abcb-5ecd8307accd', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_0cvh5ds&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for 10c7a71b-7e26-4c0e-b64c-452b66b19f3a@localhost:14064. Idle timeout: 10 min. Current group: 14e4cf4c-c559-49ac-add7-2cc2822f3cf3\n2025-12-09 02:45:53,547 245 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:53,562 260 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:53,610 308 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:53,611 309 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:53,611 309 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:53,611 309 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:53,611 309 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:53,611 309 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:53,916 614 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:54,056 754 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (140ms total) [0 unknowns]\n2025-12-09 02:45:54,088 786 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:54,446 1144 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:54,654 1352 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:54,659 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:54,659 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:54,659 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:54,659 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:54,659 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:54,659 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:54,724 1422 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:54,862 1560 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:54,869 1567 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_0cvh5ds&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:45:54,879 1577 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_0cvh5ds&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:54,889 1587 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_0cvh5ds&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:54,914 1612 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:54,963 1661 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5040\n2025-12-09 02:45:54,966 1664 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_0cvh5ds&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:54,969 1667 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:54,969 1667 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception ________ TestPopulateMetadataConfigFiles.test_delete_attach[False-None] ________ self = ns = None, attach = False @mark.parametrize("ns", [None, NSBULKANNOTATIONS, NSBULKANNOTATIONSCONFIG]) @mark.parametrize("attach", [True, False]) def test_delete_attach(self, ns, attach): > fixture = self._init_fixture_attach_cfg() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1256: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:1231: in _init_fixture_attach_cfg target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ojk9vs_f&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = '00e562ed-3419-49b8-9d9b-e25271b71b28' args = ['omero', '-s', 'localhost', '-k', '00e562ed-3419-49b8-9d9b-e25271b71b28', '-p', ...] popen = out = b'' err = b'Joined session for 9eacbf6c-ff78-49eb-a52c-c8ef82b7e044@localhost:14064. Idle timeout: 10 min. Current group: 67d049...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', '00e562ed-3419-49b8-9d9b-e25271b71b28', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ojk9vs_f&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for 9eacbf6c-ff78-49eb-a52c-c8ef82b7e044@localhost:14064. Idle timeout: 10 min. Current group: 67d049b1-4597-4fc4-a900-2d8e9c95fdf2\n2025-12-09 02:45:59,007 251 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:59,023 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:59,071 315 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:59,072 316 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:59,072 316 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:59,072 316 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:59,072 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:59,073 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:59,379 623 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:59,522 766 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (143ms total) [0 unknowns]\n2025-12-09 02:45:59,555 799 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:59,918 1162 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:46:00,122 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:46:00,127 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:46:00,127 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:46:00,127 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:46:00,127 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:46:00,127 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:46:00,127 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:46:00,191 1435 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:46:00,333 1577 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:46:00,339 1583 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ojk9vs_f&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:46:00,350 1594 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ojk9vs_f&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:46:00,359 1603 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ojk9vs_f&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:46:00,383 1627 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:46:00,427 1671 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5046\n2025-12-09 02:46:00,432 1676 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ojk9vs_f&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:00,435 1679 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:00,435 1679 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _ TestPopulateMetadataConfigFiles.test_delete_attach[False-openmicroscopy.org/omero/bulk_annotations] _ self = ns = 'openmicroscopy.org/omero/bulk_annotations', attach = False @mark.parametrize("ns", [None, NSBULKANNOTATIONS, NSBULKANNOTATIONSCONFIG]) @mark.parametrize("attach", [True, False]) def test_delete_attach(self, ns, attach): > fixture = self._init_fixture_attach_cfg() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1256: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:1231: in _init_fixture_attach_cfg target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0axtdms14&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = 'e39db856-6add-418e-95a7-3da46ca38962' args = ['omero', '-s', 'localhost', '-k', 'e39db856-6add-418e-95a7-3da46ca38962', '-p', ...] popen = out = b'' err = b'Joined session for ec9c3a15-6a9f-4795-a37f-329bd25bc517@localhost:14064. Idle timeout: 10 min. Current group: 6169eb...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.256\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'e39db856-6add-418e-95a7-3da46ca38962', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0axtdms14&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for ec9c3a15-6a9f-4795-a37f-329bd25bc517@localhost:14064. Idle timeout: 10 min. Current group: 6169eba5-ea2c-4282-9730-bd07b0f5d46e\n2025-12-09 02:46:03,835 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:46:03,851 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:46:03,900 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:46:03,901 319 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:46:03,901 319 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:46:03,901 319 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:46:03,901 319 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:46:03,902 320 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:46:04,215 633 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:46:04,357 775 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (143ms total) [0 unknowns]\n2025-12-09 02:46:04,391 809 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:46:04,755 1173 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:46:04,955 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:46:04,960 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:46:04,960 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:46:04,960 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:46:04,960 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:46:04,960 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:46:04,960 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:46:05,023 1441 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:46:05,167 1585 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:46:05,174 1592 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0axtdms14&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:46:05,184 1602 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0axtdms14&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:46:05,194 1612 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0axtdms14&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:46:05,219 1637 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:46:05,263 1681 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5052\n2025-12-09 02:46:05,271 1689 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0axtdms14&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:05,273 1691 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:05,274 1692 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.256\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception _ TestPopulateMetadataConfigFiles.test_delete_attach[False-openmicroscopy.org/omero/bulk_annotations/config] _ self = ns = 'openmicroscopy.org/omero/bulk_annotations/config', attach = False @mark.parametrize("ns", [None, NSBULKANNOTATIONS, NSBULKANNOTATIONSCONFIG]) @mark.parametrize("attach", [True, False]) def test_delete_attach(self, ns, attach): > fixture = self._init_fixture_attach_cfg() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1256: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:1231: in _init_fixture_attach_cfg target = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:247: in get_target self.plate = self.createPlate(self.rowCount, self.colCount) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_rdr2s37&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 2, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = 'fa07d210-d71d-4907-bcbc-d172f6c95cfb' args = ['omero', '-s', 'localhost', '-k', 'fa07d210-d71d-4907-bcbc-d172f6c95cfb', '-p', ...] popen = out = b'' err = b'Joined session for b4a4a50c-ee9c-4afe-a77a-6b34eb869c14@localhost:14064. Idle timeout: 10 min. Current group: 5fc264...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'fa07d210-d71d-4907-bcbc-d172f6c95cfb', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_rdr2s37&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for b4a4a50c-ee9c-4afe-a77a-6b34eb869c14@localhost:14064. Idle timeout: 10 min. Current group: 5fc264ee-2279-4ff4-8abd-6871a7b4f912\n2025-12-09 02:46:09,256 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:46:09,272 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:46:09,321 317 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:46:09,322 318 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:46:09,322 318 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:46:09,322 318 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:46:09,322 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:46:09,322 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:46:09,629 625 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:46:09,768 764 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (139ms total) [0 unknowns]\n2025-12-09 02:46:09,801 797 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:46:10,157 1153 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:46:10,361 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:46:10,366 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:46:10,366 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:46:10,366 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:46:10,366 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:46:10,366 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:46:10,366 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:46:10,428 1424 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:46:10,567 1563 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:46:10,574 1570 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_rdr2s37&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:46:10,584 1580 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_rdr2s37&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:46:10,594 1590 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_rdr2s37&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:46:10,618 1614 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:46:10,664 1660 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5058\n2025-12-09 02:46:10,670 1666 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_rdr2s37&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:10,673 1669 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:10,674 1670 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception ____________________ TestPopulateRois.testPopulateRoisPlate ____________________ self = def testPopulateRoisPlate(self): """ Create a small csv file, use populate_roi.py to parse and attach to Plate. Then query to check table has expected content. """ fixture = ROICSV() fixture.init(self) > plate = fixture.get_target() ^^^^^^^^^^^^^^^^^^^^ test/integration/metadata/test_populate.py:1424: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/metadata/test_populate.py:1409: in get_target self.plate = self.createPlate( test/integration/metadata/test_populate.py:150: in createPlate plates = self.test.import_plates(plate_rows=rowCount, ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:366: in import_plates images = self.import_fake_file(images_count=0, client=client, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:340: in import_fake_file pixel_ids = self.import_image( _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = filename = path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0fdwxb542&&plates=1&plateAcqs=1&plateCols=1&plateRows=1&fields=1.fake') client = , extra_args = None skip = 'all' kwargs = {'fields': 1, 'plateAcqs': 1, 'plateCols': 1, 'plateRows': 1, ...} server = 'localhost', port = '14064' key = 'bfe8cb88-a1a1-4426-904a-35bbb559e05f' args = ['omero', '-s', 'localhost', '-k', 'bfe8cb88-a1a1-4426-904a-35bbb559e05f', '-p', ...] popen = out = b'' err = b'Joined session for 39ec157e-88a1-4500-914e-6cc528a6b28f@localhost:14064. Idle timeout: 10 min. Current group: bc14ff...ry - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.281\n' def import_image(self, filename=None, client=None, extra_args=None, skip="all", **kwargs): """ Imports the specified file. """ if filename is None: raise Exception("No file specified") if client is None: client = self.client server = client.getProperty("omero.host") port = client.getProperty("omero.port") key = client.getSessionId() args = ["omero"] args.extend(["-s", server, "-k", key, "-p", port, "import"]) if skip: args.extend(["--skip", skip]) # Temporary fix to pass current tests by getting legacy output args.extend(["--output", "legacy"]) args.extend(["--"]) if extra_args: args.extend(extra_args) args.append(filename) popen = subprocess.Popen(args, cwd=str(self.omero_dist), stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = popen.communicate() rc = popen.wait() if rc != 0: > raise Exception("import failed: [%r] %s\n%s\n%s" % ( args, rc, out, err)) E Exception: import failed: [['omero', '-s', 'localhost', '-k', 'bfe8cb88-a1a1-4426-904a-35bbb559e05f', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0fdwxb542&&plates=1&plateAcqs=1&plateCols=1&plateRows=1&fields=1.fake')]] 2 E b'' E b'Joined session for 39ec157e-88a1-4500-914e-6cc528a6b28f@localhost:14064. Idle timeout: 10 min. Current group: bc14ffd1-3169-4f69-9e2f-960ed94e3ab6\n2025-12-09 02:46:14,118 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:46:14,133 264 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:46:14,181 312 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:46:14,182 313 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:46:14,183 314 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:46:14,183 314 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:46:14,183 314 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:46:14,183 314 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:46:14,491 622 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:46:14,632 763 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (141ms total) [0 unknowns]\n2025-12-09 02:46:14,665 796 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:46:15,023 1154 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:46:15,232 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:46:15,236 1367 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:46:15,237 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:46:15,237 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:46:15,237 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:46:15,237 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:46:15,237 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:46:15,300 1431 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:46:15,440 1571 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:46:15,446 1577 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0fdwxb542&&plates=1&plateAcqs=1&plateCols=1&plateRows=1&fields=1.fake...\n2025-12-09 02:46:15,457 1588 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0fdwxb542&&plates=1&plateAcqs=1&plateCols=1&plateRows=1&fields=1.fake\n2025-12-09 02:46:15,466 1597 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0fdwxb542&&plates=1&plateAcqs=1&plateCols=1&plateRows=1&fields=1.fake\n2025-12-09 02:46:15,510 1641 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:46:15,556 1687 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5064\n2025-12-09 02:46:15,573 1704 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0fdwxb542&&plates=1&plateAcqs=1&plateCols=1&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:15,576 1707 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:15,576 1707 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.281\n' ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:287: Exception =============================== warnings summary =============================== OmeroPy/test/integration/clitest/test_admin.py::TestAdmin::test_checkupgrade1 OmeroPy/test/integration/clitest/test_admin.py::TestAdminRestrictedAdmin::test_checkupgrade1 OmeroPy/test/integration/test_util.py::TestUpgradeCheck::testReal /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/upgrade_check.py:142: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead self.log.warn("UPGRADE AVAILABLE:" + result) OmeroPy/test/integration/clitest/test_admin.py: 2 warnings OmeroPy/test/integration/clitest/test_chgrp.py: 116 warnings OmeroPy/test/integration/clitest/test_chown.py: 76 warnings OmeroPy/test/integration/clitest/test_cleanse.py: 7 warnings OmeroPy/test/integration/clitest/test_delete.py: 81 warnings OmeroPy/test/integration/clitest/test_download.py: 19 warnings OmeroPy/test/integration/clitest/test_duplicate.py: 18 warnings OmeroPy/test/integration/clitest/test_fs.py: 23 warnings OmeroPy/test/integration/clitest/test_group.py: 154 warnings OmeroPy/test/integration/clitest/test_import.py: 173 warnings OmeroPy/test/integration/clitest/test_import_bulk.py: 1 warning OmeroPy/test/integration/clitest/test_ldap.py: 5 warnings OmeroPy/test/integration/clitest/test_metadata.py: 10 warnings OmeroPy/test/integration/clitest/test_obj.py: 56 warnings OmeroPy/test/integration/clitest/test_pyramids.py: 10 warnings OmeroPy/test/integration/clitest/test_script.py: 10 warnings OmeroPy/test/integration/clitest/test_search.py: 16 warnings OmeroPy/test/integration/clitest/test_sessions.py: 121 warnings OmeroPy/test/integration/clitest/test_tag.py: 57 warnings OmeroPy/test/integration/clitest/test_upload.py: 6 warnings OmeroPy/test/integration/clitest/test_user.py: 183 warnings /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/plugins/sessions.py:176: DeprecationWarning: OMERO_SESSION_DIR is deprecated. Use OMERO_SESSIONDIR instead. warnings.warn( OmeroPy/test/integration/clitest/test_admin.py: 4 warnings OmeroPy/test/integration/clitest/test_chgrp.py: 111 warnings OmeroPy/test/integration/clitest/test_chown.py: 77 warnings OmeroPy/test/integration/clitest/test_cleanse.py: 8 warnings OmeroPy/test/integration/clitest/test_delete.py: 81 warnings OmeroPy/test/integration/clitest/test_duplicate.py: 18 warnings OmeroPy/test/integration/clitest/test_group.py: 60 warnings OmeroPy/test/integration/clitest/test_metadata.py: 2 warnings OmeroPy/test/integration/clitest/test_pyramids.py: 102 warnings OmeroPy/test/integration/clitest/test_sessions.py: 6 warnings OmeroPy/test/integration/fstest/test_rename.py: 18 warnings OmeroPy/test/integration/gatewaytest/test_annotation.py: 56 warnings OmeroPy/test/integration/gatewaytest/test_chgrp.py: 17 warnings OmeroPy/test/integration/gatewaytest/test_chmod.py: 29 warnings OmeroPy/test/integration/gatewaytest/test_chown.py: 2 warnings OmeroPy/test/integration/gatewaytest/test_config_service.py: 42 warnings OmeroPy/test/integration/gatewaytest/test_connection.py: 6 warnings OmeroPy/test/integration/gatewaytest/test_delete.py: 12 warnings OmeroPy/test/integration/gatewaytest/test_fs.py: 12 warnings OmeroPy/test/integration/gatewaytest/test_get_objects.py: 39 warnings OmeroPy/test/integration/gatewaytest/test_image.py: 6 warnings OmeroPy/test/integration/gatewaytest/test_image_wrapper.py: 6 warnings OmeroPy/test/integration/gatewaytest/test_missing_pyramid.py: 6 warnings OmeroPy/test/integration/gatewaytest/test_pixels.py: 6 warnings OmeroPy/test/integration/gatewaytest/test_plate_wrapper.py: 6 warnings OmeroPy/test/integration/gatewaytest/test_rdefs.py: 6 warnings OmeroPy/test/integration/gatewaytest/test_search_objects.py: 6 warnings OmeroPy/test/integration/gatewaytest/test_services.py: 18 warnings OmeroPy/test/integration/gatewaytest/test_user.py: 10 warnings OmeroPy/test/integration/gatewaytest/test_wrapper.py: 9 warnings OmeroPy/test/integration/metadata/test_populate.py: 161 warnings OmeroPy/test/integration/test_annotationPermissions.py: 8 warnings OmeroPy/test/integration/test_chgrp.py: 37 warnings OmeroPy/test/integration/test_chmod.py: 1 warning OmeroPy/test/integration/test_chown.py: 2 warnings OmeroPy/test/integration/test_cmdcallback.py: 6 warnings OmeroPy/test/integration/test_delete.py: 28 warnings OmeroPy/test/integration/test_isession.py: 5 warnings OmeroPy/test/integration/test_iupdate.py: 1 warning OmeroPy/test/integration/test_mail.py: 2 warnings OmeroPy/test/integration/test_permissions.py: 3 warnings OmeroPy/test/integration/test_reimport.py: 7 warnings OmeroPy/test/integration/test_repository.py: 18 warnings /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/callbacks.py:270: DeprecationWarning: isSet() is deprecated, use is_set() instead return self.event.isSet() OmeroPy/test/integration/clitest/test_delete.py::TestDelete::testInputWithElisionDefault[1] OmeroPy/test/integration/clitest/test_delete.py::TestDelete::testInputWithElisionDefault[2] OmeroPy/test/integration/clitest/test_delete.py::TestDelete::testInputWithElisionDefault[3] /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/cli.py:2105: DeprecationWarning: Using '--dry-run'. Future versions will switch to '--force'. Explicitly set the parameter for portability warnings.warn("\nUsing '--dry-run'.\ OmeroPy/test/integration/clitest/test_import.py::TestImport::testAutoClose OmeroPy/test/integration/clitest/test_import.py::TestImport::testAutoClose OmeroPy/test/integration/clitest/test_import.py::TestImport::testAutoClose OmeroPy/test/integration/clitest/test_import.py::TestImport::testAutoClose /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/clients.py:1019: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead self.__logger.warn( OmeroPy/test/integration/clitest/test_import_bulk.py::TestImportBulk::testBulk /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_import_bulk.py:131: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testBulk1') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_obj.py::TestObj::test_get_unit_and_value /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_model_PixelsI.py:37: DeprecationWarning: Pixels.relatedTo is deprecated warnings.warn(item + " is deprecated", DeprecationWarning) OmeroPy/test/integration/clitest/test_script.py: 2 warnings OmeroPy/test/integration/scriptstest/test_cli.py: 8 warnings OmeroPy/test/integration/scriptstest/test_inputs.py: 1 warning OmeroPy/test/integration/scriptstest/test_ping.py: 6 warnings OmeroPy/test/integration/scriptstest/test_rand.py: 1 warning OmeroPy/test/integration/test_scripts.py: 11 warnings /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/callbacks.py:89: DeprecationWarning: isSet() is deprecated, use is_set() instead if self.event.isSet(): OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testLogin[None-True] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testLogin_None_True_0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testLogin[None-False] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testLogin_None_False_0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testLogin[300-True] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testLogin_300_True_0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testLogin[300-False] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testLogin_300_False_0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testLoginAs[rw----] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testLoginAs_rw_____0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testLoginAs[rwr---] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testLoginAs_rwr____0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testLoginAs[rwra--] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testLoginAs_rwra___0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testLoginAs[rwrw--] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testLoginAs_rwrw___0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testLoginMultiGroup[True-True] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testLoginMultiGroup_True_True_0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testLoginMultiGroup[True-False] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testLoginMultiGroup_True_False0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testLoginMultiGroup[False-True] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testLoginMultiGroup_False_True0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testLoginMultiGroup[False-False] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testLoginMultiGroup_False_Fals0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testGroup /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testGroup0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testTimeout /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testTimeout0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testFile /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testFile0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testKey /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testKey0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testWho[user] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testWho_user_0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::testWho[root] /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/testWho_root_0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::test_open /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/test_open0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::test_open_with_id /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/test_open_with_id0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::test_open_restricted_admin_no_sudo /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/test_open_restricted_admin_no_0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::test_open_restricted_admin_sudo /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/test_open_restricted_admin_sud0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/clitest/test_sessions.py::TestSessions::test_close /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/clitest/test_sessions.py:36: PytestWarning: Value of environment variable OMERO_SESSIONDIR type should be str, but got local('/tmp/pytest-of-omero/pytest-60/test_close0') (type: LocalPath); converted to str implicitly monkeypatch.setenv("OMERO_SESSIONDIR", tmpdir) OmeroPy/test/integration/gatewaytest/test_annotation.py: 4 warnings OmeroPy/test/integration/gatewaytest/test_chmod.py: 28 warnings OmeroPy/test/integration/gatewaytest/test_connection.py: 10 warnings OmeroPy/test/integration/gatewaytest/test_get_objects.py: 4 warnings OmeroPy/test/integration/gatewaytest/test_image_wrapper.py: 3 warnings OmeroPy/test/integration/gatewaytest/test_user.py: 1 warning /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py:4855: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead logger.warn("%s on %s to <%s> %s(%r, %r)", OmeroPy/test/integration/gatewaytest/test_delete.py::TestDelete::testDeleteObjectDirect /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py:4426: DeprecationWarning: Deprecated. Use deleteObject() or deleteObjects() warnings.warn( OmeroPy/test/integration/gatewaytest/test_fs.py::TestFileset::testGetArchivedFiles OmeroPy/test/integration/gatewaytest/test_fs.py::TestFileset::testGetArchivedFiles OmeroPy/test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testGetArchivedFiles OmeroPy/test/integration/gatewaytest/test_fs.py::TestArchivedOriginalFiles::testGetArchivedFiles /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py:10315: DeprecationWarning: Deprecated. Use getImportedImageFiles() warnings.warn( OmeroPy/test/integration/gatewaytest/test_get_objects.py::TestLeaderAndMemberOfGroup::testGroupSummaryAsOwnerDeprecated OmeroPy/test/integration/gatewaytest/test_get_objects.py::TestLeaderAndMemberOfGroup::testGroupSummaryAsOwnerDeprecated OmeroPy/test/integration/gatewaytest/test_get_objects.py::TestLeaderAndMemberOfGroup::testGroupSummaryAsMemberDeprecated OmeroPy/test/integration/gatewaytest/test_get_objects.py::TestLeaderAndMemberOfGroup::testGroupSummaryAsMemberDeprecated /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py:3108: DeprecationWarning: Deprecated. Use ExperimenterGroupWrapper.groupSummary() warnings.warn( OmeroPy/test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[None-Dataset2Images1Missing] OmeroPy/test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[1-Dataset2Images1Missing] OmeroPy/test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[10-Dataset2Images1Missing] /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/populate_metadata.py:955: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead log.warn( OmeroPy/test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[None-Dataset2Images1Missing] OmeroPy/test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[1-Dataset2Images1Missing] OmeroPy/test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[10-Dataset2Images1Missing] /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/populate_metadata.py:1389: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead log.warn("Invalid Id:%d found in row %s", row[n], row) OmeroPy/test/integration/scriptsharness/test_harness.py::TestScriptsViaOmeroCli::testDefinition OmeroPy/test/integration/scriptsharness/test_harness.py::TestScriptsViaOmeroCli::testDefinition OmeroPy/test/integration/scriptsharness/test_harness.py::TestScriptsViaOmeroCli::testSimpleScript OmeroPy/test/integration/scriptsharness/test_harness.py::TestScriptsViaOmeroCli::testSimpleScript :70: DeprecationWarning: This plugin is deprecated as of OMERO 5.5.0. Use the upload CLI plugin available from https://pypi.org/project/omero-upload/ instead. OmeroPy/test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_numpy_save_as_image[True-tiff] /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/_pytest/unraisableexception.py:67: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/usr/lib64/python3.11/tempfile.py", line 467, in __del__ self.close() File "/usr/lib64/python3.11/tempfile.py", line 463, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp56kqu1ua.tiff' Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) OmeroPy/test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_numpy_save_as_image[True-tiff] /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/_pytest/unraisableexception.py:67: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/usr/lib64/python3.11/tempfile.py", line 467, in __del__ self.close() File "/usr/lib64/python3.11/tempfile.py", line 463, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpsoioj695.tiff' Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) OmeroPy/test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_numpy_save_as_image[True-tiff] /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/_pytest/unraisableexception.py:67: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/usr/lib64/python3.11/tempfile.py", line 467, in __del__ self.close() File "/usr/lib64/python3.11/tempfile.py", line 463, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpko54f_y6.tiff' Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) OmeroPy/test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_numpy_save_as_image[True-foo] /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/_pytest/unraisableexception.py:67: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/usr/lib64/python3.11/tempfile.py", line 467, in __del__ self.close() File "/usr/lib64/python3.11/tempfile.py", line 463, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmphaxe0x8n.foo' Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) OmeroPy/test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_numpy_save_as_image[True-foo] /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/_pytest/unraisableexception.py:67: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/usr/lib64/python3.11/tempfile.py", line 467, in __del__ self.close() File "/usr/lib64/python3.11/tempfile.py", line 463, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpvlbulgkz.foo' Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) OmeroPy/test/integration/scriptstest/test_script_utils.py::TestScriptUtils::test_numpy_save_as_image[True-foo] /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/_pytest/unraisableexception.py:67: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/usr/lib64/python3.11/tempfile.py", line 467, in __del__ self.close() File "/usr/lib64/python3.11/tempfile.py", line 463, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpjowy48g2.foo' Enable tracemalloc to get traceback where the object was allocated. See https://docs.pytest.org/en/stable/how-to/capture-warnings.html#resource-warnings for more info. warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) OmeroPy/test/integration/test_isession.py::TestISession::testSessionWithIP[127.0.0.1] /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_model_SessionI.py:37: DeprecationWarning: Session.userIP is deprecated warnings.warn(item + " is deprecated", DeprecationWarning) OmeroPy/test/integration/test_rawpixelsstore.py: 110 warnings /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/test/integration/test_rawpixelsstore.py:197: DeprecationWarning: isSet() is deprecated, use is_set() instead while not event.isSet() and self.success < 10: OmeroPy/test/integration/test_repository.py::TestPythonImporter::testImportFileset OmeroPy/test/integration/test_repository.py::TestPythonImporter::testImportsFrom2Groups OmeroPy/test/integration/test_repository.py::TestPythonImporter::testImportsFrom2Groups OmeroPy/test/integration/test_repository.py::TestOriginalMetadata::testFakeImport /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:1318: DeprecationWarning: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead. NamedValue('locale', locale.getdefaultlocale()[0])) OmeroPy/test/integration/test_scripts.py::TestScripts::testRunScript OmeroPy/test/integration/test_scripts.py::TestScripts::testRunScript /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/decorators.py:82: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead log.warn( OmeroPy/test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testThumbs OmeroPy/test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testThumbs OmeroPy/test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testThumbs OmeroPy/test/integration/test_tickets1000.py::TestTicket1000::test880 /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/script_utils.py:1308: DeprecationWarning: This method is deprecated as of OMERO 5.3.0 warnings.warn( OmeroPy/test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testThumbs OmeroPy/test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testThumbs OmeroPy/test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testThumbs OmeroPy/test/integration/test_tickets1000.py::TestTicket1000::test880 /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/script_utils.py:1069: DeprecationWarning: This method is deprecated as of OMERO 5.3.0. Use upload_plane instead warnings.warn( OmeroPy/test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testThumbs OmeroPy/test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testThumbs OmeroPy/test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testThumbs OmeroPy/test/integration/test_tickets1000.py::TestTicket1000::test880 /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/script_utils.py:1254: DeprecationWarning: This method is deprecated as of OMERO 5.3.0. Use reset_rendering_settings warnings.warn( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html - generated xml file: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/target/reports/integration/junit-results.xml - =========================== short test summary info ============================ FAILED test/integration/clitest/test_download.py::TestDownload::testPolicyGlobalRestriction[+read,+write,+image] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '0aefab47-fab3-463b-a2ff-58a7477d82e9', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_05ndztjpl&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake')]] 2 b'' b'Joined session for 2081d0af-e14a-4c35-a9ad-e04e05759504@localhost:14064. Idle timeout: 10 min. Current group: d365c2f3-8d08-427b-a843-c0535eafc66f\n2025-12-09 02:07:23,720 243 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:07:23,735 258 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:07:23,782 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:07:23,783 306 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:07:23,783 306 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:07:23,784 307 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:07:23,784 307 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:07:23,784 307 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:07:24,090 613 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:07:24,262 785 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 170ms. (172ms total) [0 unknowns]\n2025-12-09 02:07:24,296 819 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:07:24,690 1213 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:07:24,898 1421 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:07:24,907 1430 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:07:24,907 1430 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:07:24,907 1430 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:07:24,907 1430 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:07:24,907 1430 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:07:24,907 1430 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:07:24,969 1492 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:07:25,107 1630 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:07:25,113 1636 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_05ndztjpl&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake...\n2025-12-09 02:07:25,123 1646 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_05ndztjpl&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:25,133 1656 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_05ndztjpl&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:25,158 1681 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:07:25,202 1725 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3663\n2025-12-09 02:07:25,213 1736 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_05ndztjpl&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:25,216 1739 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:25,216 1739 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.252\n' FAILED test/integration/clitest/test_download.py::TestDownload::testPolicyGroupRestriction[+read,+write,+image] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '4bf90eca-96e3-46b4-8230-11fabdd0ff7f', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0xz5skwee&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake')]] 2 b'' b'Joined session for 97a63a67-153f-402a-a086-2285fbaff207@localhost:14064. Idle timeout: 10 min. Current group: 5d0c18ff-148b-4670-8206-1980d5452996\n2025-12-09 02:07:28,530 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:07:28,545 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:07:28,594 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:07:28,595 317 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:07:28,595 317 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:07:28,595 317 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:07:28,595 317 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:07:28,595 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:07:28,907 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:07:29,049 771 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (142ms total) [0 unknowns]\n2025-12-09 02:07:29,082 804 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:07:29,444 1166 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:07:29,646 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:07:29,651 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:07:29,651 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:07:29,651 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:07:29,651 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:07:29,651 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:07:29,651 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:07:29,715 1437 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:07:29,869 1591 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:07:29,875 1597 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0xz5skwee&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake...\n2025-12-09 02:07:29,886 1608 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0xz5skwee&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:29,896 1618 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0xz5skwee&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:29,919 1641 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:07:29,963 1685 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3669\n2025-12-09 02:07:29,965 1687 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0xz5skwee&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:29,968 1690 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:29,968 1690 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.259\n' FAILED test/integration/clitest/test_download.py::TestDownload::testPolicyGroupRestriction[-read,-write,-image,-plate] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '52c7ec3b-9f7a-4027-a8de-614922620f94', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0l_pmwi_z&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake')]] 2 b'' b'Joined session for 783ca543-3fed-45fd-9163-6c6881f797d2@localhost:14064. Idle timeout: 10 min. Current group: a15252c6-3a2c-4136-9119-bdb3953f1ebe\n2025-12-09 02:07:33,014 240 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:07:33,029 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:07:33,077 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:07:33,077 303 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:07:33,078 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:07:33,078 304 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:07:33,078 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:07:33,078 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:07:33,377 603 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:07:33,514 740 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 135ms. (137ms total) [0 unknowns]\n2025-12-09 02:07:33,546 772 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:07:33,900 1126 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:07:34,100 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:07:34,104 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:07:34,104 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:07:34,104 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:07:34,104 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:07:34,104 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:07:34,104 1330 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:07:34,166 1392 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:07:34,307 1533 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:07:34,314 1540 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0l_pmwi_z&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake...\n2025-12-09 02:07:34,321 1547 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0l_pmwi_z&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:34,329 1555 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0l_pmwi_z&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:34,354 1580 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:07:34,402 1628 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3675\n2025-12-09 02:07:34,405 1631 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0l_pmwi_z&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:34,407 1633 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:34,408 1634 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.247\n' FAILED test/integration/clitest/test_download.py::TestDownload::testPolicyGroupRestriction[-read,+write,+image,-plate] - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'abc69e1e-204b-4428-a7ef-23d9bb431c59', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ahr9l1n4&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake')]] 2 b'' b'Joined session for 6b843102-4d25-48c4-b781-e1729fb4230a@localhost:14064. Idle timeout: 10 min. Current group: 31f27dd0-8283-4faa-9920-72b94ac4faad\n2025-12-09 02:07:37,574 243 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:07:37,589 258 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:07:37,637 306 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:07:37,638 307 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:07:37,638 307 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:07:37,638 307 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:07:37,638 307 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:07:37,638 307 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:07:37,939 608 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:07:38,078 747 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (139ms total) [0 unknowns]\n2025-12-09 02:07:38,111 780 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:07:38,466 1135 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:07:38,663 1332 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:07:38,667 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:07:38,667 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:07:38,667 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:07:38,667 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:07:38,667 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:07:38,667 1336 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:07:38,730 1399 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:07:38,883 1552 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:07:38,889 1558 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ahr9l1n4&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake...\n2025-12-09 02:07:38,900 1569 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ahr9l1n4&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:38,909 1578 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ahr9l1n4&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:38,935 1604 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:07:38,982 1651 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3681\n2025-12-09 02:07:38,985 1654 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ahr9l1n4&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:38,988 1657 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:38,988 1657 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.263\n' FAILED test/integration/clitest/test_download.py::TestDownload::testPolicyGroupRestriction[+read,+write,+image,-plate] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '1dfe714c-5b0b-4c14-b013-5f62569c953f', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0yskgiw8r&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake')]] 2 b'' b'Joined session for bc4b85e3-e9fa-489e-971e-48db1694bdd3@localhost:14064. Idle timeout: 10 min. Current group: e7ab896e-abd6-4f22-8814-6ce2afc7a5c8\n2025-12-09 02:07:42,112 243 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:07:42,126 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:07:42,173 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:07:42,174 305 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:07:42,174 305 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:07:42,175 306 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:07:42,175 306 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:07:42,175 306 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:07:42,475 606 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:07:42,614 745 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 135ms. (138ms total) [0 unknowns]\n2025-12-09 02:07:42,646 777 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:07:42,999 1130 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:07:43,206 1337 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:07:43,211 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:07:43,211 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:07:43,211 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:07:43,211 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:07:43,211 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:07:43,211 1342 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:07:43,275 1406 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:07:43,441 1572 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:07:43,448 1579 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0yskgiw8r&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake...\n2025-12-09 02:07:43,462 1593 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0yskgiw8r&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:43,472 1603 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0yskgiw8r&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:43,508 1639 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:07:43,563 1694 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3687\n2025-12-09 02:07:43,567 1698 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0yskgiw8r&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:43,570 1701 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:43,570 1701 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.300\n' FAILED test/integration/clitest/test_download.py::TestDownload::testPolicyGroupRestriction[+read,+write,+image,+plate] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '15dfdade-80f5-4687-86aa-c52571f1fc47', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0gnltwgta&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake')]] 2 b'' b'Joined session for 14d2a7ad-e4b4-4b85-9db3-18ac372b643a@localhost:14064. Idle timeout: 10 min. Current group: 82001f58-a256-457c-b131-b8d264af8aa6\n2025-12-09 02:07:46,728 257 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:07:46,744 273 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:07:46,794 323 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:07:46,795 324 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:07:46,795 324 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:07:46,795 324 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:07:46,795 324 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:07:46,795 324 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:07:47,108 637 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:07:47,258 787 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 148ms. (150ms total) [0 unknowns]\n2025-12-09 02:07:47,292 821 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:07:47,665 1194 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:07:47,864 1393 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:07:47,867 1396 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:07:47,867 1396 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:07:47,868 1397 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:07:47,868 1397 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:07:47,868 1397 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:07:47,868 1397 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:07:47,938 1467 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:07:48,076 1605 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:07:48,083 1612 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0gnltwgta&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake...\n2025-12-09 02:07:48,093 1622 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0gnltwgta&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:48,174 1703 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0gnltwgta&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\n2025-12-09 02:07:48,198 1727 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:07:48,243 1772 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3693\n2025-12-09 02:07:48,246 1775 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0gnltwgta&&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:48,249 1778 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:07:48,249 1778 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.318\n' FAILED test/integration/clitest/test_fs.py::TestFS::testImportTime[all-True] - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'ce69d5c2-f820-4c38-87b9-bb3f009cc56b', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_82o_yo6dy&series=8&plateCols=2&plateRows=2&fields=2.fake')]] 2 b'' b'Joined session for e22ad704-9b78-43a4-bedc-bd5b6f010b2a@localhost:14064. Idle timeout: 10 min. Current group: 6286f4d5-541b-4b66-bc28-3f264ea96577\n2025-12-09 02:08:13,246 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:08:13,261 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:08:13,309 313 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:08:13,310 314 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:08:13,310 314 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:08:13,310 314 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:08:13,310 314 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:08:13,311 315 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:08:13,620 624 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:08:13,766 770 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 144ms. (147ms total) [0 unknowns]\n2025-12-09 02:08:13,799 803 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:08:14,157 1161 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:08:14,357 1361 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:08:14,362 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:08:14,362 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:08:14,362 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:08:14,362 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:08:14,362 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:08:14,362 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:08:14,424 1428 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:08:14,557 1561 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:08:14,564 1568 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_82o_yo6dy&series=8&plateCols=2&plateRows=2&fields=2.fake...\n2025-12-09 02:08:14,573 1577 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_82o_yo6dy&series=8&plateCols=2&plateRows=2&fields=2.fake\n2025-12-09 02:08:14,583 1587 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_82o_yo6dy&series=8&plateCols=2&plateRows=2&fields=2.fake\n2025-12-09 02:08:14,606 1610 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:08:14,650 1654 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3717\n2025-12-09 02:08:14,653 1657 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_82o_yo6dy&series=8&plateCols=2&plateRows=2&fields=2.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:08:14,656 1660 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:08:14,656 1660 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.237\n' FAILED test/integration/clitest/test_fs.py::TestFS::testImportTime[minmax-True] - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'ce69d5c2-f820-4c38-87b9-bb3f009cc56b', '-p', '14064', 'import', '--skip', 'minmax', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8kou3t36k&series=8&plateCols=2&plateRows=2&fields=2.fake')]] 2 b'' b'Joined session for e22ad704-9b78-43a4-bedc-bd5b6f010b2a@localhost:14064. Idle timeout: 10 min. Current group: 6286f4d5-541b-4b66-bc28-3f264ea96577\n2025-12-09 02:08:19,112 240 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:08:19,127 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:08:19,175 303 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:08:19,175 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:08:19,176 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:08:19,475 603 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:08:19,618 746 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (143ms total) [0 unknowns]\n2025-12-09 02:08:19,650 778 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:08:20,004 1132 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:08:20,213 1341 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:08:20,218 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:08:20,218 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:08:20,218 1346 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:08:20,219 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:08:20,219 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:08:20,219 1347 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:08:20,317 1445 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:08:20,455 1583 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:08:20,465 1593 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8kou3t36k&series=8&plateCols=2&plateRows=2&fields=2.fake...\n2025-12-09 02:08:20,474 1602 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8kou3t36k&series=8&plateCols=2&plateRows=2&fields=2.fake\n2025-12-09 02:08:20,510 1638 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8kou3t36k&series=8&plateCols=2&plateRows=2&fields=2.fake\n2025-12-09 02:08:20,535 1663 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:08:20,583 1711 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3723\n2025-12-09 02:08:20,585 1713 [l.Client-0] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8kou3t36k&series=8&plateCols=2&plateRows=2&fields=2.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:08:20,588 1716 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:08:20,588 1716 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.278\n' FAILED test/integration/clitest/test_fs.py::TestFS::testImportTime[thumbnails-True] - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'ce69d5c2-f820-4c38-87b9-bb3f009cc56b', '-p', '14064', 'import', '--skip', 'thumbnails', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8k_3bxeq0&series=8&plateCols=2&plateRows=2&fields=2.fake')]] 2 b'' b'Joined session for e22ad704-9b78-43a4-bedc-bd5b6f010b2a@localhost:14064. Idle timeout: 10 min. Current group: 6286f4d5-541b-4b66-bc28-3f264ea96577\n2025-12-09 02:08:25,281 256 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:08:25,297 272 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:08:25,347 322 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:08:25,347 322 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:08:25,348 323 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:08:25,660 635 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:08:25,809 784 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 146ms. (149ms total) [0 unknowns]\n2025-12-09 02:08:25,842 817 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:08:26,214 1189 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:08:26,413 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:08:26,417 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:08:26,417 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:08:26,417 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:08:26,417 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:08:26,417 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:08:26,417 1392 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:08:26,520 1495 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:08:26,657 1632 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:08:26,666 1641 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8k_3bxeq0&series=8&plateCols=2&plateRows=2&fields=2.fake...\n2025-12-09 02:08:26,675 1650 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8k_3bxeq0&series=8&plateCols=2&plateRows=2&fields=2.fake\n2025-12-09 02:08:26,685 1660 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8k_3bxeq0&series=8&plateCols=2&plateRows=2&fields=2.fake\n2025-12-09 02:08:26,708 1683 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:08:26,753 1728 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 3729\n2025-12-09 02:08:26,757 1732 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_8k_3bxeq0&series=8&plateCols=2&plateRows=2&fields=2.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:08:26,759 1734 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:08:26,760 1735 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.246\n' FAILED test/integration/clitest/test_import.py::TestImport::testTargetArgument[source0-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testTargetArgument[source1-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testTargetArgument[source2-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testTargetArgument[source3-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testTargetArgument[source4-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testTargetArgument[source5-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[+-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[--True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[%-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testQualifiedNameModelTargetArgument[@-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[+-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[--True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[%-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testQualifiedNameTemplateTargetArgument[@-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testMultipleNameModelTargets[-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testMultipleNameModelTargets[+-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testMultipleNameModelTargets[--True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNestedNameTemplateTargetArgument[True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testMultipleNameTemplateTargetArgument[-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testMultipleNameTemplateTargetArgument[+-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testMultipleNameTemplateTargetArgument[--True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testMultipleNameTemplateTargetArgument[@-True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testUniqueMultipleNameTemplateTargetArgument[True] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testImportOutputDefaultWithScreen[1] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testImportOutputDefaultWithScreen[2] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testImportOutputDefaultWithScreen[3] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate-x] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--description] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--plate_description] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate-n] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate-n-x] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate-n--description] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate-n--plate_description] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--name] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--name-x] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--name--description] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--name--plate_description] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--plate_name] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--plate_name-x] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--plate_name--description] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testNamingArguments[Plate--plate_name--plate_description] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/gatewaytest/test_user.py::TestUser::testSaveAs - ValueError: invalid literal for int() with base 10: b'' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[None-Screen2Plates] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ph6h8nxm&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:05,235 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:05,250 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:05,297 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:05,298 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:05,298 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:05,298 304 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:05,298 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:05,298 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:05,598 604 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:05,737 743 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (139ms total) [0 unknowns]\n2025-12-09 02:44:05,769 775 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:06,161 1167 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:06,357 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:06,362 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:06,362 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:06,362 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:06,362 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:06,362 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:06,362 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:06,424 1430 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:06,568 1574 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:06,575 1581 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ph6h8nxm&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:44:06,586 1592 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ph6h8nxm&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:06,595 1601 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ph6h8nxm&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:06,621 1627 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:06,667 1673 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4926\n2025-12-09 02:44:06,675 1681 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ph6h8nxm&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:06,678 1684 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:06,678 1684 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.259\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[None-Plate2Wells] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_076rz4ikh&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:08,219 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:08,234 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:08,281 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:08,282 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:08,282 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:08,282 304 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:08,283 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:08,283 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:08,582 604 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:08,721 743 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 136ms. (139ms total) [0 unknowns]\n2025-12-09 02:44:08,753 775 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:09,110 1132 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:09,312 1334 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:09,317 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:09,317 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:09,317 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:09,317 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:09,317 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:09,317 1339 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:09,380 1402 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:09,516 1538 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:09,522 1544 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_076rz4ikh&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:44:09,533 1555 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_076rz4ikh&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:09,541 1563 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_076rz4ikh&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:09,567 1589 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:09,610 1632 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4929\n2025-12-09 02:44:09,617 1639 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_076rz4ikh&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:09,620 1642 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:09,620 1642 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.245\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[1-Screen2Plates] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_02tc7yfco&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:36,629 241 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:36,644 256 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:36,691 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:36,692 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:36,692 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:36,692 304 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:36,692 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:36,692 304 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:37,005 617 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:37,151 763 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 144ms. (146ms total) [0 unknowns]\n2025-12-09 02:44:37,186 798 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:37,559 1171 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:37,771 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:37,776 1388 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:37,777 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:37,777 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:37,777 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:37,777 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:37,777 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:37,841 1453 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:37,991 1603 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:37,998 1610 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_02tc7yfco&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:44:38,010 1622 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_02tc7yfco&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:38,019 1631 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_02tc7yfco&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:38,044 1656 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:38,090 1702 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4955\n2025-12-09 02:44:38,093 1705 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_02tc7yfco&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:38,095 1707 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:38,096 1708 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.260\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[1-Plate2Wells] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0r_0f_nyz&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:39,661 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:39,676 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:39,723 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:39,724 305 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:39,724 305 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:39,724 305 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:39,724 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:39,724 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:40,025 606 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:40,165 746 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (140ms total) [0 unknowns]\n2025-12-09 02:44:40,197 778 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:40,547 1128 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:40,743 1324 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:40,748 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:40,748 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:40,748 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:40,748 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:40,748 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:40,748 1329 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:40,817 1398 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:40,992 1573 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:40,998 1579 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0r_0f_nyz&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:44:41,010 1591 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0r_0f_nyz&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:41,019 1600 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0r_0f_nyz&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:41,051 1632 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:41,095 1676 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4958\n2025-12-09 02:44:41,101 1682 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0r_0f_nyz&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:41,104 1685 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:41,104 1685 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.292\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[10-Screen2Plates] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0sl62cvm4&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:48,431 244 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:48,448 261 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:48,497 310 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:48,497 310 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:48,498 311 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:48,498 311 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:48,498 311 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:48,498 311 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:48,803 616 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:48,945 758 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (142ms total) [0 unknowns]\n2025-12-09 02:44:48,978 791 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:49,343 1156 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:49,545 1358 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:49,556 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:49,556 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:49,556 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:49,556 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:49,556 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:49,556 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:49,622 1435 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:49,755 1568 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:49,762 1575 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0sl62cvm4&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:44:49,772 1585 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0sl62cvm4&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:49,781 1594 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0sl62cvm4&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:49,805 1618 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:49,852 1665 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4966\n2025-12-09 02:44:49,855 1668 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0sl62cvm4&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:49,858 1671 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:49,858 1671 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.241\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadata[10-Plate2Wells] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_048tz9q5r&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:51,431 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:51,447 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:51,495 313 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:51,496 314 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:51,496 314 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:51,496 314 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:51,496 314 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:51,496 314 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:51,804 622 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:51,946 764 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (143ms total) [0 unknowns]\n2025-12-09 02:44:51,979 797 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:52,339 1157 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:52,540 1358 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:52,545 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:52,546 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:52,546 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:52,546 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:52,546 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:52,546 1364 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:52,610 1428 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:52,758 1576 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:52,765 1583 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_048tz9q5r&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:44:52,776 1594 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_048tz9q5r&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:52,785 1603 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_048tz9q5r&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:44:52,810 1628 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:52,857 1675 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4969\n2025-12-09 02:44:52,863 1681 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_048tz9q5r&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:52,866 1684 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:52,867 1685 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.262\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadataNsAnns[Plate2WellsNs] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0v46p221w&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 b'' b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:44:57,869 247 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:44:57,884 262 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:44:57,933 311 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:44:57,934 312 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:44:57,934 312 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:44:57,934 312 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:44:57,934 312 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:44:57,934 312 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:44:58,241 619 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:44:58,388 766 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 144ms. (147ms total) [0 unknowns]\n2025-12-09 02:44:58,421 799 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:44:58,770 1148 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:44:58,971 1349 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:44:58,977 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:44:58,977 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:44:58,977 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:44:58,977 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:44:58,977 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:44:58,977 1355 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:44:59,040 1418 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:44:59,195 1573 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:44:59,202 1580 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0v46p221w&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:44:59,214 1592 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0v46p221w&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:44:59,224 1602 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0v46p221w&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:44:59,256 1634 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:44:59,302 1680 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4977\n2025-12-09 02:44:59,306 1684 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0v46p221w&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:59,308 1686 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:44:59,309 1687 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.274\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadataNsAnns[Plate2WellsNs2] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_04jmzhh03&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 b'' b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:45:00,885 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:00,900 264 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:00,948 312 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:00,949 313 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:00,949 313 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:00,949 313 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:00,949 313 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:00,949 313 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:01,259 623 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:01,405 769 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 144ms. (146ms total) [0 unknowns]\n2025-12-09 02:45:01,438 802 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:01,799 1163 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:02,005 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:02,010 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:02,010 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:02,010 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:02,010 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:02,010 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:02,010 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:02,080 1444 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:02,231 1595 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:02,238 1602 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_04jmzhh03&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:02,250 1614 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_04jmzhh03&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:02,259 1623 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_04jmzhh03&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:02,283 1647 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:02,331 1695 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4980\n2025-12-09 02:45:02,337 1701 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_04jmzhh03&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:02,340 1704 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:02,340 1704 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.265\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadataNsAnnsUnavailableHeader - Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0i7c31p6_&&plates=1&plateAcqs=1&plateCols=2&plateRows=2&fields=1.fake')]] 2 b'' b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:45:03,899 240 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:03,914 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:03,963 304 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:03,963 304 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:03,964 305 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:03,964 305 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:03,964 305 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:03,964 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:04,264 605 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:04,404 745 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (140ms total) [0 unknowns]\n2025-12-09 02:45:04,436 777 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:04,790 1131 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:04,980 1321 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:04,984 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:04,985 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:04,985 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:04,985 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:04,985 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:04,985 1326 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:05,052 1393 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:05,189 1530 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:05,196 1537 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0i7c31p6_&&plates=1&plateAcqs=1&plateCols=2&plateRows=2&fields=1.fake...\n2025-12-09 02:45:05,206 1547 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0i7c31p6_&&plates=1&plateAcqs=1&plateCols=2&plateRows=2&fields=1.fake\n2025-12-09 02:45:05,217 1558 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0i7c31p6_&&plates=1&plateAcqs=1&plateCols=2&plateRows=2&fields=1.fake\n2025-12-09 02:45:05,242 1583 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:05,289 1630 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4983\n2025-12-09 02:45:05,293 1634 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0i7c31p6_&&plates=1&plateAcqs=1&plateCols=2&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:05,295 1636 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:05,296 1637 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.248\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadata::testPopulateMetadataNsAnnsFail - Exception: import failed: [['omero', '-s', 'localhost', '-k', '13ded21a-bbf1-454f-82f5-7627467b5007', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_00jtdq09t&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for b11a00d4-0d27-47cf-b272-72177d10a441@localhost:14064. Idle timeout: 10 min. Current group: c94d2633-1ce7-4e48-a40e-b17216a5d820\n2025-12-09 02:45:06,854 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:06,870 266 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:06,918 314 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:06,919 315 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:06,920 316 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:06,920 316 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:06,920 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:06,920 316 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:07,229 625 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:07,373 769 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 142ms. (144ms total) [0 unknowns]\n2025-12-09 02:45:07,406 802 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:07,764 1160 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:07,971 1367 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:07,976 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:07,976 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:07,976 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:07,976 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:07,976 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:07,976 1372 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:08,041 1437 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:08,177 1573 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:08,184 1580 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_00jtdq09t&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:45:08,195 1591 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_00jtdq09t&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:08,204 1600 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_00jtdq09t&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:08,229 1625 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:08,276 1672 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4986\n2025-12-09 02:45:08,280 1676 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_00jtdq09t&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:08,283 1679 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:08,283 1679 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.247\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadataDedup::testPopulateMetadataNsAnnsDedup[None] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '3a8ef545-99b6-4cca-af45-f2cc0dfaa304', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0k10bqkuc&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 b'' b'Joined session for 30ddef33-19ad-48c2-b930-80249024ea58@localhost:14064. Idle timeout: 10 min. Current group: 0dc1629f-b52b-415a-aa24-b48de9cb4b9a\n2025-12-09 02:45:12,157 250 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:12,172 265 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:12,221 314 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:12,222 315 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:12,222 315 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:12,222 315 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:12,222 315 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:12,223 316 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:12,535 628 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:12,682 775 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 145ms. (148ms total) [0 unknowns]\n2025-12-09 02:45:12,715 808 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:13,070 1163 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:13,265 1358 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:13,275 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:13,275 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:13,275 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:13,275 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:13,275 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:13,275 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:13,340 1433 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:13,483 1576 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:13,489 1582 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0k10bqkuc&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:13,499 1592 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0k10bqkuc&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:13,508 1601 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0k10bqkuc&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:13,532 1625 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:13,578 1671 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4992\n2025-12-09 02:45:13,586 1679 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0k10bqkuc&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:13,589 1682 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:13,589 1682 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.254\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadataDedup::testPopulateMetadataNsAnnsDedup[openmicroscopy.org/omero/bulk_annotations] - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'e41045b2-76e8-47ef-9546-b92781542fb7', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09o9xsynh&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 b'' b'Joined session for aa934116-76dd-492a-95fa-44044c3670e5@localhost:14064. Idle timeout: 10 min. Current group: c4ba8cba-9dcf-42e7-bc8d-3ea57739afb4\n2025-12-09 02:45:17,059 254 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:17,075 270 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:17,125 320 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:17,126 321 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:17,126 321 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:17,126 321 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:17,126 321 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:17,126 321 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:17,438 633 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:17,586 781 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 145ms. (147ms total) [0 unknowns]\n2025-12-09 02:45:17,619 814 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:17,986 1181 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:18,189 1384 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:18,195 1390 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:18,195 1390 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:18,195 1390 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:18,195 1390 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:18,195 1390 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:18,195 1390 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:18,259 1454 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:18,415 1610 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:18,422 1617 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09o9xsynh&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:18,434 1629 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09o9xsynh&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:18,444 1639 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09o9xsynh&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:18,470 1665 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:18,516 1711 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4998\n2025-12-09 02:45:18,522 1717 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09o9xsynh&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:18,525 1720 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:18,525 1720 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.271\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadataDedup::testPopulateMetadataNsAnnsDedup[openmicroscopy.org/mapr/gene] - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'da5d3db1-b278-4026-af58-2ca45b4ee5aa', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0mv9kpgka&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 b'' b'Joined session for 6e715598-2f14-4765-9e6e-511c8f2f3158@localhost:14064. Idle timeout: 10 min. Current group: 789ae208-8cdb-4356-947a-1fbc69da502b\n2025-12-09 02:45:22,642 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:22,658 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:22,707 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:22,708 319 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:22,708 319 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:22,708 319 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:22,708 319 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:22,708 319 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:23,018 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:23,167 778 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 146ms. (148ms total) [0 unknowns]\n2025-12-09 02:45:23,200 811 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:23,566 1177 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:23,775 1386 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:23,780 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:23,780 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:23,780 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:23,780 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:23,780 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:23,780 1391 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:23,845 1456 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:23,986 1597 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:23,994 1605 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0mv9kpgka&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:24,005 1616 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0mv9kpgka&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:24,015 1626 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0mv9kpgka&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:24,040 1651 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:24,085 1696 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5004\n2025-12-09 02:45:24,091 1702 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0mv9kpgka&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:24,094 1705 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:24,094 1705 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.254\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadataDedup::testPopulateMetadataNsAnnsDedupDelete[None] - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'ea377c36-4ed2-4eb5-9e61-74b7ecec841d', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0f2se96od&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 b'' b'Joined session for d72dc75c-40d1-4813-a5d3-1cb4580108d5@localhost:14064. Idle timeout: 10 min. Current group: 5e1a75b6-55e9-4267-bcbe-9ecb3e00cd8d\n2025-12-09 02:45:27,602 240 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:27,617 255 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:27,664 302 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:27,665 303 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:27,665 303 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:27,665 303 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:27,665 303 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:27,665 303 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:27,965 603 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:28,107 745 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (143ms total) [0 unknowns]\n2025-12-09 02:45:28,140 778 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:28,489 1127 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:28,683 1321 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:28,687 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:28,687 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:28,687 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:28,687 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:28,687 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:28,687 1325 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:28,756 1394 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:28,896 1534 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:28,903 1541 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0f2se96od&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:28,914 1552 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0f2se96od&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:28,924 1562 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0f2se96od&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:28,949 1587 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:28,993 1631 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5010\n2025-12-09 02:45:29,000 1638 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0f2se96od&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:29,003 1641 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:29,004 1642 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.253\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadataDedup::testPopulateMetadataNsAnnsDedupDelete[openmicroscopy.org/omero/bulk_annotations] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '3f0c1530-1d7d-42f8-aa43-16f5a5b0bcf6', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0reqs0fco&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 b'' b'Joined session for e5b46dd1-505c-452f-addd-d23a99fc6b54@localhost:14064. Idle timeout: 10 min. Current group: ea5c7eff-3b4b-4c15-910b-c5368a72084e\n2025-12-09 02:45:33,039 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:33,054 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:33,103 317 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:33,104 318 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:33,104 318 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:33,104 318 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:33,104 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:33,104 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:33,415 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:33,563 777 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 145ms. (148ms total) [0 unknowns]\n2025-12-09 02:45:33,596 810 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:33,956 1170 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:34,155 1369 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:34,160 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:34,160 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:34,160 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:34,160 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:34,160 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:34,160 1374 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:34,231 1445 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:34,374 1588 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:34,381 1595 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0reqs0fco&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:34,392 1606 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0reqs0fco&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:34,403 1617 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0reqs0fco&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:34,428 1642 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:34,474 1688 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5016\n2025-12-09 02:45:34,483 1697 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0reqs0fco&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:34,485 1699 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:34,486 1700 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.260\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadataDedup::testPopulateMetadataNsAnnsDedupDelete[openmicroscopy.org/mapr/gene] - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'c7d8d047-cd0b-4360-a6f6-60a2f110ca4e', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0b_u563ji&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake')]] 2 b'' b'Joined session for c9d80c0c-eff8-4d52-8673-c951237cbf9f@localhost:14064. Idle timeout: 10 min. Current group: b559e526-0796-4719-af16-2a027d1705d2\n2025-12-09 02:45:37,891 288 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:37,907 304 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:37,956 353 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:37,957 354 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:37,957 354 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:37,957 354 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:37,957 354 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:37,957 354 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:38,270 667 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:38,420 817 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 148ms. (150ms total) [0 unknowns]\n2025-12-09 02:45:38,456 853 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:38,831 1228 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:39,041 1438 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:39,046 1443 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:39,047 1444 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:39,047 1444 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:39,047 1444 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:39,047 1444 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:39,047 1444 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:39,112 1509 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:39,250 1647 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:39,257 1654 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0b_u563ji&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake...\n2025-12-09 02:45:39,269 1666 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0b_u563ji&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:39,278 1675 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0b_u563ji&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\n2025-12-09 02:45:39,303 1700 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:39,350 1747 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5022\n2025-12-09 02:45:39,353 1750 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0b_u563ji&&plates=1&plateAcqs=1&plateCols=4&plateRows=2&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:39,356 1753 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:39,356 1753 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadataConfigFiles::test_delete_attach[True-None] - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'e7b5f762-b3ed-4e47-b0e8-934c8424014a', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09tyx960k&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for c45563c1-d7f3-4a67-8c1a-20944565052c@localhost:14064. Idle timeout: 10 min. Current group: fa861828-ce40-4006-bb17-ee602134a2f7\n2025-12-09 02:45:43,393 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:43,409 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:43,457 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:43,458 317 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:43,458 317 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:43,458 317 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:43,459 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:43,459 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:43,770 629 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:43,913 772 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 141ms. (143ms total) [0 unknowns]\n2025-12-09 02:45:43,946 805 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:44,315 1174 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:44,518 1377 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:44,522 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:44,522 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:44,522 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:44,522 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:44,522 1381 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:44,523 1382 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:44,584 1443 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:44,723 1582 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:44,730 1589 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09tyx960k&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:45:44,740 1599 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09tyx960k&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:44,750 1609 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09tyx960k&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:44,773 1632 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:44,817 1676 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5028\n2025-12-09 02:45:44,823 1682 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_09tyx960k&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:44,826 1685 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:44,826 1685 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.246\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadataConfigFiles::test_delete_attach[True-openmicroscopy.org/omero/bulk_annotations] - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'd502e2d2-ebdf-4332-a089-72798e1c63f2', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_01wwkwsq9&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for 81243c9b-054c-49d1-bd53-2bf76ce3fb5e@localhost:14064. Idle timeout: 10 min. Current group: ea97bf3e-c06e-48e3-853d-04064c37de69\n2025-12-09 02:45:48,712 256 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:48,727 271 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:48,777 321 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:48,778 322 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:48,778 322 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:48,778 322 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:48,778 322 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:48,778 322 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:49,088 632 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:49,232 776 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 142ms. (143ms total) [0 unknowns]\n2025-12-09 02:45:49,265 809 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:49,632 1176 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:49,834 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:49,839 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:49,839 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:49,839 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:49,839 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:49,839 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:49,839 1383 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:49,902 1446 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:50,063 1607 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:50,070 1614 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_01wwkwsq9&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:45:50,080 1624 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_01wwkwsq9&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:50,089 1633 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_01wwkwsq9&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:50,114 1658 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:50,159 1703 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5034\n2025-12-09 02:45:50,163 1707 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_01wwkwsq9&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:50,166 1710 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:50,167 1711 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.270\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadataConfigFiles::test_delete_attach[True-openmicroscopy.org/omero/bulk_annotations/config] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '3b96e06c-01b5-403d-abcb-5ecd8307accd', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_0cvh5ds&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for 10c7a71b-7e26-4c0e-b64c-452b66b19f3a@localhost:14064. Idle timeout: 10 min. Current group: 14e4cf4c-c559-49ac-add7-2cc2822f3cf3\n2025-12-09 02:45:53,547 245 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:53,562 260 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:53,610 308 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:53,611 309 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:53,611 309 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:53,611 309 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:53,611 309 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:53,611 309 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:53,916 614 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:54,056 754 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (140ms total) [0 unknowns]\n2025-12-09 02:45:54,088 786 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:54,446 1144 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:45:54,654 1352 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:45:54,659 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:45:54,659 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:45:54,659 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:45:54,659 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:45:54,659 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:45:54,659 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:45:54,724 1422 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:45:54,862 1560 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:45:54,869 1567 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_0cvh5ds&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:45:54,879 1577 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_0cvh5ds&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:54,889 1587 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_0cvh5ds&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:45:54,914 1612 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:45:54,963 1661 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5040\n2025-12-09 02:45:54,966 1664 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_0cvh5ds&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:54,969 1667 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:45:54,969 1667 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadataConfigFiles::test_delete_attach[False-None] - Exception: import failed: [['omero', '-s', 'localhost', '-k', '00e562ed-3419-49b8-9d9b-e25271b71b28', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ojk9vs_f&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for 9eacbf6c-ff78-49eb-a52c-c8ef82b7e044@localhost:14064. Idle timeout: 10 min. Current group: 67d049b1-4597-4fc4-a900-2d8e9c95fdf2\n2025-12-09 02:45:59,007 251 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:45:59,023 267 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:45:59,071 315 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:45:59,072 316 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:45:59,072 316 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:45:59,072 316 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:45:59,072 316 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:45:59,073 317 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:45:59,379 623 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:45:59,522 766 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (143ms total) [0 unknowns]\n2025-12-09 02:45:59,555 799 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:45:59,918 1162 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:46:00,122 1366 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:46:00,127 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:46:00,127 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:46:00,127 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:46:00,127 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:46:00,127 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:46:00,127 1371 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:46:00,191 1435 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:46:00,333 1577 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:46:00,339 1583 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ojk9vs_f&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:46:00,350 1594 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ojk9vs_f&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:46:00,359 1603 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ojk9vs_f&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:46:00,383 1627 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:46:00,427 1671 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5046\n2025-12-09 02:46:00,432 1676 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0ojk9vs_f&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:00,435 1679 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:00,435 1679 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadataConfigFiles::test_delete_attach[False-openmicroscopy.org/omero/bulk_annotations] - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'e39db856-6add-418e-95a7-3da46ca38962', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0axtdms14&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for ec9c3a15-6a9f-4795-a37f-329bd25bc517@localhost:14064. Idle timeout: 10 min. Current group: 6169eba5-ea2c-4282-9730-bd07b0f5d46e\n2025-12-09 02:46:03,835 253 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:46:03,851 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:46:03,900 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:46:03,901 319 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:46:03,901 319 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:46:03,901 319 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:46:03,901 319 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:46:03,902 320 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:46:04,215 633 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:46:04,357 775 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 140ms. (143ms total) [0 unknowns]\n2025-12-09 02:46:04,391 809 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:46:04,755 1173 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:46:04,955 1373 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:46:04,960 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:46:04,960 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:46:04,960 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:46:04,960 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:46:04,960 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:46:04,960 1378 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:46:05,023 1441 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:46:05,167 1585 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:46:05,174 1592 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0axtdms14&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:46:05,184 1602 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0axtdms14&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:46:05,194 1612 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0axtdms14&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:46:05,219 1637 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:46:05,263 1681 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5052\n2025-12-09 02:46:05,271 1689 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0axtdms14&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:05,273 1691 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:05,274 1692 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.256\n' FAILED test/integration/metadata/test_populate.py::TestPopulateMetadataConfigFiles::test_delete_attach[False-openmicroscopy.org/omero/bulk_annotations/config] - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'fa07d210-d71d-4907-bcbc-d172f6c95cfb', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_rdr2s37&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for b4a4a50c-ee9c-4afe-a77a-6b34eb869c14@localhost:14064. Idle timeout: 10 min. Current group: 5fc264ee-2279-4ff4-8abd-6871a7b4f912\n2025-12-09 02:46:09,256 252 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:46:09,272 268 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:46:09,321 317 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:46:09,322 318 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:46:09,322 318 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:46:09,322 318 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:46:09,322 318 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:46:09,322 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:46:09,629 625 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:46:09,768 764 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 137ms. (139ms total) [0 unknowns]\n2025-12-09 02:46:09,801 797 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:46:10,157 1153 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:46:10,361 1357 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:46:10,366 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:46:10,366 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:46:10,366 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:46:10,366 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:46:10,366 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:46:10,366 1362 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:46:10,428 1424 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:46:10,567 1563 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:46:10,574 1570 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_rdr2s37&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake...\n2025-12-09 02:46:10,584 1580 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_rdr2s37&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:46:10,594 1590 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_rdr2s37&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\n2025-12-09 02:46:10,618 1614 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:46:10,664 1660 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5058\n2025-12-09 02:46:10,670 1666 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0_rdr2s37&&plates=1&plateAcqs=1&plateCols=2&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 0\n\tat java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)\n\tat java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)\n\tat java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)\n\tat java.base/java.util.Objects.checkIndex(Objects.java:374)\n\tat java.base/java.util.ArrayList.remove(ArrayList.java:536)\n\tat ome.xml.model.ReferenceList.remove(ReferenceList.java:102)\n\tat ome.xml.model.ReferenceList.set(ReferenceList.java:129)\n\tat ome.xml.model.PlateAcquisition.setLinkedWellSample(PlateAcquisition.java:341)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setPlateAcquisitionWellSampleRef(OMEXMLMetadataImpl.java:12003)\n\tat ome.xml.meta.FilterMetadata.setPlateAcquisitionWellSampleRef(FilterMetadata.java:2264)\n\tat ome.xml.meta.MetadataConverter.convertPlates(MetadataConverter.java:2426)\n\tat ome.xml.meta.MetadataConverter.convertMetadata(MetadataConverter.java:100)\n\tat loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:924)\n\tat loci.formats.in.FakeReader.populateSPW(FakeReader.java:1532)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:932)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=Index 1 out of bounds for length 0}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:10,673 1669 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:10,674 1670 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.250\n' FAILED test/integration/metadata/test_populate.py::TestPopulateRois::testPopulateRoisPlate - Exception: import failed: [['omero', '-s', 'localhost', '-k', 'bfe8cb88-a1a1-4426-904a-35bbb559e05f', '-p', '14064', 'import', '--skip', 'all', '--output', 'legacy', '--', path('/home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0fdwxb542&&plates=1&plateAcqs=1&plateCols=1&plateRows=1&fields=1.fake')]] 2 b'' b'Joined session for 39ec157e-88a1-4500-914e-6cc528a6b28f@localhost:14064. Idle timeout: 10 min. Current group: bc14ffd1-3169-4f69-9e2f-960ed94e3ab6\n2025-12-09 02:46:14,118 249 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT\n2025-12-09 02:46:14,133 264 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025\n2025-12-09 02:46:14,181 312 [ main] INFO formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64\n2025-12-09 02:46:14,182 313 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping thumbnails creation\n2025-12-09 02:46:14,183 314 [ main] INFO formats.importer.cli.CommandLineImporter - Skipping minimum/maximum computation\n2025-12-09 02:46:14,183 314 [ main] INFO formats.importer.cli.CommandLineImporter - Disabling upgrade check\n2025-12-09 02:46:14,183 314 [ main] INFO formats.importer.cli.CommandLineImporter - Setting output format: legacy\n2025-12-09 02:46:14,183 314 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO\n2025-12-09 02:46:14,491 622 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM\n2025-12-09 02:46:14,632 763 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 138ms. (141ms total) [0 unknowns]\n2025-12-09 02:46:14,665 796 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064\n2025-12-09 02:46:15,023 1154 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back\n2025-12-09 02:46:15,232 1363 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.\n2025-12-09 02:46:15,236 1367 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3\n2025-12-09 02:46:15,237 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT\n2025-12-09 02:46:15,237 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25\n2025-12-09 02:46:15,237 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux\n2025-12-09 02:46:15,237 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64\n2025-12-09 02:46:15,237 1368 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64\n2025-12-09 02:46:15,300 1431 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION\n2025-12-09 02:46:15,440 1571 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START\n2025-12-09 02:46:15,446 1577 [3-thread-1] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0fdwxb542&&plates=1&plateAcqs=1&plateCols=1&plateRows=1&fields=1.fake...\n2025-12-09 02:46:15,457 1588 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0fdwxb542&&plates=1&plateAcqs=1&plateCols=1&plateRows=1&fields=1.fake\n2025-12-09 02:46:15,466 1597 [3-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0fdwxb542&&plates=1&plateAcqs=1&plateCols=1&plateRows=1&fields=1.fake\n2025-12-09 02:46:15,510 1641 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END\n2025-12-09 02:46:15,556 1687 [2-thread-1] INFO ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 5064\n2025-12-09 02:46:15,573 1704 [l.Client-1] ERROR ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION: /home/omero/omero/tmp/omero_omero/2234817/import_fake_file_0fdwxb542&&plates=1&plateAcqs=1&plateCols=1&plateRows=1&fields=1.fake\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\njava.lang.RuntimeException: Failure response on import!\nCategory: ::omero::grid::ImportRequest\nName: error-on-init\nParameters: {stacktrace=java.lang.NullPointerException\n\tat ome.xml.model.LightPath.linkEmissionFilter(LightPath.java:296)\n\tat ome.xml.meta.OMEXMLMetadataImpl.setLightPathEmissionFilterRef(OMEXMLMetadataImpl.java:9214)\n\tat ome.xml.meta.FilterMetadata.setLightPathEmissionFilterRef(FilterMetadata.java:1498)\n\tat loci.formats.in.FakeReader.fillInstrumentRefs(FakeReader.java:1221)\n\tat loci.formats.in.FakeReader.initFile(FakeReader.java:984)\n\tat loci.formats.FormatReader.setId(FormatReader.java:1480)\n\tat loci.formats.ImageReader.setId(ImageReader.java:864)\n\tat ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelFiller.setId(ChannelFiller.java:258)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat loci.formats.Memoizer.setId(Memoizer.java:726)\n\tat loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)\n\tat ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:412)\n\tat ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:763)\n\tat ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:245)\n\tat omero.cmd.HandleI.steps(HandleI.java:438)\n\tat omero.cmd.HandleI$RunSteps.innerWork(HandleI.java:509)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:383)\n\tat omero.cmd.HandleI$2.doWork(HandleI.java:380)\n\tat jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.security.basic.EventHandler.invoke(EventHandler.java:154)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\n\tat org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy74.doWork(Unknown Source)\n\tat ome.services.util.Executor$Impl.execute(Executor.java:447)\n\tat omero.cmd.HandleI.run(HandleI.java:379)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat ome.services.util.Executor$Impl$1.call(Executor.java:488)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n, message=}\n\n\tat ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:807)\n\tat omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)\n\tat omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)\n\tat omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:15,576 1707 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import\njava.lang.Exception: Import failure\n\tat ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:701)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:354)\n\tat ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)\n\tat java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)\n\tat java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n2025-12-09 02:46:15,576 1707 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error\n\n==> Summary\n1 file uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:00.281\n' ERROR test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testClose - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_connection.py::TestConnectionMethods::testTopLevelObjects - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testThumbnail - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testThumbnailSet - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testRenderingModels - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testSplitChannel - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testLinePlots - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testProjections - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testProperties - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testPixelSizeUnits - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testUnitsGetValue - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testChannelWavelengthUnits - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testExposureTimeUnits - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testShortname - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testImageDate - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testSimpleMarshal - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testExport - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testRenderJpegRegion - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testRenderJpegRegion_resolution - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testRenderJpegRegion_invalid_resolution - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testRenderBirdsEyeView - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_image.py::TestImage::testRenderBirdsEyeView_Size - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_pixels.py::TestPixels::testReuseRawPixelsStore - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_pixels.py::TestPixels::testPlaneInfo - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_pixels.py::TestPixels::testPixelsType - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_pixels.py::TestPixels::testGetTile - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_pixels.py::TestPixels::testGetPlane - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_pixels.py::TestPixels::testGetPlanesExceptionOnGetPlane - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_pixels.py::TestPixels::testGetPlanesExceptionOnClose - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_pixels.py::TestPixels::testGetPlanesExceptionOnBoth - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_pixels.py::TestPixels::testGetHistogram - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testDefault - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testCustomized - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testChannelWindows - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testFloatDefaultMinMax - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testEmissionWave - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testBatchCopy - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testGroupBasedPermissions - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testGetRdefs - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testResetDefaults - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testQuantizationSettings - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testQuantizationSettingsInvalid - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testQuantizationSettingsBulk - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testGetChannelsNoRE - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testSetActiveChannelsNoRE - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testSetActiveChannelsWithRE - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::test_set_active_channels_set_inactive[True] - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::test_set_active_channels_set_inactive[False] - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testUnregisterService - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testRegisterService - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_rdefs.py::TestRDefs::testCloseRE - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_wrapper.py::TestWrapper::testAllObjectsWrapped - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_wrapper.py::TestWrapper::testDatasetWrapper - ValueError: invalid literal for int() with base 10: b'' ERROR test/integration/gatewaytest/test_wrapper.py::TestWrapper::testDetailsWrapper - ValueError: invalid literal for int() with base 10: b'' = 77 failed, 1868 passed, 9 skipped, 36 deselected, 2472 warnings, 54 errors in 4583.00s (1:16:23) = !! 12/09/25 03:18:04.981 error: 249 communicators not destroyed during global destruction. Result: 1 BUILD SUCCESSFUL Total time: 76 minutes 29 seconds + /home/omero/workspace/OMERO-test-integration/src/build.py -f components/tools/OmeroFS/build.xml integration -Dtestreports.dir=target/reports/integration Buildfile: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroFS/build.xml Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroFS... python-integration: Created dir: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroFS/target/reports/integration ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-9.0.2, pluggy-1.6.0 -- /home/omero/workspace/OMERO-test-integration/.venv3/bin/python3.11 cachedir: .pytest_cache django: version: 5.2.9, settings: omeroweb.settings (from ini) rootdir: /home/omero/workspace/OMERO-test-integration/src/components/tools configfile: pytest.ini plugins: xdist-3.8.0, mock-3.15.1, django-4.11.1 collecting ... collected 1 item test/integration/test_dbclient.py::TestDropBoxClient::test1 PASSED [100%] - generated xml file: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroFS/target/reports/integration/junit-results.xml - ============================== 1 passed in 0.06s =============================== BUILD SUCCESSFUL Total time: 1 second + /home/omero/workspace/OMERO-test-integration/src/build.py -f components/tools/OmeroWeb/build.xml integration -Dtestreports.dir=target/reports/integration Buildfile: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroWeb/build.xml Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroWeb... Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroWeb... python-integration: Created dir: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroWeb/target/reports/integration ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-9.0.2, pluggy-1.6.0 -- /home/omero/workspace/OMERO-test-integration/.venv3/bin/python3.11 cachedir: .pytest_cache django: version: 5.2.9, settings: omeroweb.settings (from ini) rootdir: /home/omero/workspace/OMERO-test-integration/src/components/tools configfile: pytest.ini plugins: xdist-3.8.0, mock-3.15.1, django-4.11.1 collecting ... collected 440 items test/integration/test_annotate.py::TestMapAnnotations::test_annotate_map PASSED [ 0%] test/integration/test_annotate.py::TestTagging::test_create_tag PASSED [ 0%] test/integration/test_annotate.py::TestTagging::test_annotate_tag PASSED [ 0%] test/integration/test_annotate.py::TestBatchAnnotate::test_batch_annotate_tag PASSED [ 0%] test/integration/test_annotate.py::TestFileAnnotations::test_add_fileannotations_form PASSED [ 1%] test/integration/test_annotate.py::TestFileAnnotations::test_batch_add_fileannotations[1] PASSED [ 1%] test/integration/test_annotate.py::TestFileAnnotations::test_batch_add_fileannotations[2] PASSED [ 1%] test/integration/test_api_containers.py::TestContainers::test_create_update_unsupported[method0-Plate] PASSED [ 1%] test/integration/test_api_containers.py::TestContainers::test_create_update_unsupported[method0-Image] PASSED [ 2%] test/integration/test_api_containers.py::TestContainers::test_create_update_unsupported[method0-Well] PASSED [ 2%] test/integration/test_api_containers.py::TestContainers::test_create_update_unsupported[method0-Channel] PASSED [ 2%] test/integration/test_api_containers.py::TestContainers::test_create_update_unsupported[method0-foo] PASSED [ 2%] test/integration/test_api_containers.py::TestContainers::test_create_update_unsupported[method1-Plate] PASSED [ 2%] test/integration/test_api_containers.py::TestContainers::test_create_update_unsupported[method1-Image] PASSED [ 3%] test/integration/test_api_containers.py::TestContainers::test_create_update_unsupported[method1-Well] PASSED [ 3%] test/integration/test_api_containers.py::TestContainers::test_create_update_unsupported[method1-Channel] PASSED [ 3%] test/integration/test_api_containers.py::TestContainers::test_create_update_unsupported[method1-foo] PASSED [ 3%] test/integration/test_api_containers.py::TestContainers::test_delete_unsupported[Plate] PASSED [ 4%] test/integration/test_api_containers.py::TestContainers::test_delete_unsupported[Image] PASSED [ 4%] test/integration/test_api_containers.py::TestContainers::test_delete_unsupported[Well] PASSED [ 4%] test/integration/test_api_containers.py::TestContainers::test_container_crud[Project] PASSED [ 4%] test/integration/test_api_containers.py::TestContainers::test_container_crud[Dataset] PASSED [ 5%] test/integration/test_api_containers.py::TestContainers::test_container_crud[Screen] PASSED [ 5%] test/integration/test_api_containers.py::TestContainers::test_datasets_plates[Dataset-True] PASSED [ 5%] test/integration/test_api_containers.py::TestContainers::test_datasets_plates[Dataset-False] PASSED [ 5%] test/integration/test_api_containers.py::TestContainers::test_datasets_plates[Plate-True] PASSED [ 5%] test/integration/test_api_containers.py::TestContainers::test_datasets_plates[Plate-False] PASSED [ 6%] test/integration/test_api_containers.py::TestContainers::test_screens PASSED [ 6%] test/integration/test_api_containers.py::TestContainers::test_screen_plates_update PASSED [ 6%] test/integration/test_api_containers.py::TestContainers::test_container_tags_update[dtype0] PASSED [ 6%] test/integration/test_api_containers.py::TestContainers::test_container_tags_update[dtype1] PASSED [ 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test/integration/test_api_login.py::TestLogin::test_login_errors[application/json-credentials1] PASSED [ 15%] test/integration/test_api_login.py::TestLogin::test_login_errors[application/json-credentials2] PASSED [ 16%] test/integration/test_api_login.py::TestLogin::test_login_errors[application/json-credentials3] PASSED [ 16%] test/integration/test_api_login.py::TestLogin::test_login_errors[application/json-credentials4] PASSED [ 16%] test/integration/test_api_login.py::TestLogin::test_login_example[multipart/form-data; boundary=BoUnDaRyStRiNg] PASSED [ 16%] test/integration/test_api_login.py::TestLogin::test_login_example[application/json] PASSED [ 17%] test/integration/test_api_projects.py::TestProjects::test_marshal_projects_not_logged_in PASSED [ 17%] test/integration/test_api_projects.py::TestProjects::test_marshal_projects_no_results PASSED [ 17%] test/integration/test_api_projects.py::TestProjects::test_marshal_projects_user PASSED [ 17%] 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[ 22%] test/integration/test_chgrp.py::TestChgrp::test_chgrp_new_container[admin] PASSED [ 22%] test/integration/test_chgrp.py::TestChgrp::test_chgrp_old_container[user] PASSED [ 23%] test/integration/test_chgrp.py::TestChgrp::test_chgrp_old_container[admin] PASSED [ 23%] test/integration/test_chown.py::TestChown::test_chown_dry_run[admin] PASSED [ 23%] test/integration/test_config.py::test_flattenProperties PASSED [ 23%] test/integration/test_config.py::TestConfig::testDefaultConfig PASSED [ 24%] test/integration/test_config.py::TestConfig::testDefaultConfigConversion PASSED [ 24%] test/integration/test_config.py::TestConfig::testUpgradeDropdownMenuConfig[foo-colleagues.label] PASSED [ 24%] test/integration/test_config.py::TestConfig::testUpgradeDropdownMenuConfig[foo-leaders.label] PASSED [ 24%] test/integration/test_config.py::TestConfig::testUpgradeDropdownMenuConfig[foo-everyone.label] PASSED [ 25%] test/integration/test_containers.py::TestContainers::test_add_and_rename_container PASSED [ 25%] test/integration/test_containers.py::TestContainers::test_add_owned_container PASSED [ 25%] test/integration/test_containers.py::TestContainers::test_paste_move_remove_deletamany_image PASSED [ 25%] test/integration/test_containers.py::TestContainers::test_edit_share PASSED [ 25%] test/integration/test_csrf.py::TestCsrf::test_csrf_middleware_enabled PASSED [ 26%] test/integration/test_csrf.py::TestCsrf::test_forgot_password PASSED [ 26%] test/integration/test_csrf.py::TestCsrf::test_move_data PASSED [ 26%] test/integration/test_csrf.py::TestCsrf::test_add_and_remove_comment PASSED [ 26%] test/integration/test_csrf.py::TestCsrf::test_attach_file PASSED [ 27%] test/integration/test_csrf.py::TestCsrf::test_edit_channel_names PASSED [ 27%] test/integration/test_csrf.py::TestCsrf::test_copy_past_rendering_settings PASSED [ 27%] test/integration/test_csrf.py::TestCsrf::test_reset_rendering_settings PASSED [ 27%] 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test/integration/test_download.py::TestDownload::test_spw_download PASSED [ 30%] test/integration/test_download.py::TestDownload::test_orphaned_image_direct_download PASSED [ 31%] test/integration/test_download.py::TestDownload::test_orphaned_image_download PASSED [ 31%] test/integration/test_download.py::TestDownload::test_image_in_dataset_download PASSED [ 31%] test/integration/test_download.py::TestDownload::test_image_in_dataset_in_project_download PASSED [ 31%] test/integration/test_download.py::TestDownload::test_well_download PASSED [ 32%] test/integration/test_download.py::TestDownload::test_attachment_download PASSED [ 32%] test/integration/test_download.py::TestDownloadAs::test_download_image_as[jpeg] PASSED [ 32%] test/integration/test_download.py::TestDownloadAs::test_download_image_as[png] PASSED [ 32%] test/integration/test_download.py::TestDownloadAs::test_download_image_as[tif] PASSED [ 32%] test/integration/test_download.py::TestDownloadAs::test_download_images_as_zip[jpeg] PASSED [ 33%] test/integration/test_download.py::TestDownloadAs::test_download_images_as_zip[png] PASSED [ 33%] test/integration/test_download.py::TestDownloadAs::test_download_images_as_zip[tif] PASSED [ 33%] test/integration/test_groups_users.py::TestGroupsUsers::test_group_users_menu PASSED [ 33%] test/integration/test_histogram.py::TestHistogram::test_histogram_bin_count[None] PASSED [ 34%] test/integration/test_histogram.py::TestHistogram::test_histogram_bin_count[10] PASSED [ 34%] test/integration/test_history.py::TestHistory::test_history PASSED [ 34%] test/integration/test_history.py::TestHistory::test_calendar_default PASSED [ 34%] test/integration/test_history.py::TestHistory::test_calendar_month PASSED [ 35%] test/integration/test_links.py::TestLinks::test_link_project_datasets PASSED [ 35%] test/integration/test_links.py::TestLinks::test_link_datasets_images PASSED [ 35%] test/integration/test_links.py::TestLinks::test_link_unlink_tagset_tags PASSED [ 35%] test/integration/test_links.py::TestLinks::test_unlink_screen_plate PASSED [ 35%] test/integration/test_login.py::TestLogin::test_login_errors[credentials0] PASSED [ 36%] test/integration/test_login.py::TestLogin::test_login_errors[credentials1] PASSED [ 36%] test/integration/test_login.py::TestLogin::test_login_errors[credentials2] PASSED [ 36%] test/integration/test_login.py::TestLogin::test_login_errors[credentials3] PASSED [ 36%] test/integration/test_login.py::TestLogin::test_get_login_page PASSED [ 37%] test/integration/test_login.py::TestLogin::test_login_redirect[] PASSED [ 37%] test/integration/test_login.py::TestLogin::test_login_redirect[/webclient/usertags/] PASSED [ 37%] test/integration/test_login.py::TestLogin::test_login_view PASSED [ 37%] test/integration/test_marshal.py::TestImgDetail::test_image_detail PASSED [ 37%] test/integration/test_metadata.py::TestCoreMetadata::test_pixel_size_units PASSED [ 38%] test/integration/test_metadata.py::TestCoreMetadata::test_none_pixel_size PASSED [ 38%] test/integration/test_metadata.py::TestBulkAnnotations::test_nsbulkannotations_file[True] PASSED [ 38%] test/integration/test_metadata.py::TestBulkAnnotations::test_nsbulkannotations_file[False] PASSED [ 38%] test/integration/test_metadata.py::TestBulkAnnotations::test_nsbulkannotations_not_file PASSED [ 39%] test/integration/test_plategrid.py::TestPlateGrid::test_get_plate_grid_metadata[shrink] PASSED [ 39%] test/integration/test_plategrid.py::TestPlateGrid::test_get_plate_grid_metadata[trim] PASSED [ 39%] test/integration/test_plategrid.py::TestPlateGrid::test_get_plate_grid_metadata[expand] PASSED [ 39%] test/integration/test_plategrid.py::TestPlateGrid::test_well_images PASSED [ 40%] test/integration/test_plategrid.py::TestPlateGrid::test_instantiation PASSED [ 40%] test/integration/test_plategrid.py::TestPlateGrid::test_metadata_grid_size PASSED [ 40%] test/integration/test_plategrid.py::TestPlateGrid::test_metadata_thumbnail_url PASSED [ 40%] test/integration/test_plategrid.py::TestPlateGrid::test_full_grid PASSED [ 40%] test/integration/test_plategrid.py::TestPlateGrid::test_acquisition_date PASSED [ 41%] test/integration/test_plategrid.py::TestPlateGrid::test_creation_date PASSED [ 41%] test/integration/test_plategrid.py::TestPlateGrid::test_description PASSED [ 41%] test/integration/test_plategrid.py::TestScreenPlateTables::test_get_plate_table PASSED [ 41%] test/integration/test_rendering.py::TestRendering::test_copy_past_rendering_settings_from_image PASSED [ 42%] test/integration/test_rendering.py::TestRendering::test_copy_past_rendering_settings_from_url PASSED [ 42%] test/integration/test_rendering.py::TestRendering::test_all_rendering_defs PASSED [ 42%] test/integration/test_rendering.py::TestRenderImageRegion::test_render_image_region_incomplete_request PASSED [ 42%] test/integration/test_rendering.py::TestRenderImageRegion::test_render_image_region_malformed_tile_argument PASSED [ 42%] test/integration/test_rendering.py::TestRenderImageRegion::test_render_image_region_malformed_region_argument PASSED [ 43%] test/integration/test_rendering.py::TestRenderImageRegion::test_render_image_region_tile_params PASSED [ 43%] test/integration/test_rendering.py::TestRenderImageRegion::test_render_image_region_tile_params_large_image PASSED [ 43%] test/integration/test_rendering.py::TestRenderImageRegion::test_render_image_region_tile_params_negative_resolution PASSED [ 43%] test/integration/test_rendering.py::TestRenderImageRegion::test_render_image_region_tile_params_invalid_resolution PASSED [ 44%] test/integration/test_rendering.py::TestRenderImageRegion::test_render_image_region_tile_params_big_image PASSED [ 44%] test/integration/test_rendering.py::TestRenderImageRegion::test_render_image_region_region_params PASSED [ 44%] test/integration/test_rendering.py::TestRenderImageRegion::test_render_image_region_region_params_big_image PASSED [ 44%] test/integration/test_rendering.py::TestRenderImageRegion::test_render_birds_eye_view_big_image PASSED [ 45%] test/integration/test_rendering.py::TestRenderImageRegion::test_render_image_region_big_image_resolution PASSED [ 45%] test/integration/test_scripts.py::TestScripts::test_script_ui_defaults PASSED [ 45%] test/integration/test_scripts.py::TestScripts::test_script_inputs_outputs[inputs0] PASSED [ 45%] test/integration/test_scripts.py::TestScripts::test_script_inputs_outputs[inputs1] PASSED [ 45%] test/integration/test_scripts.py::TestScripts::test_script_inputs_outputs[inputs2] PASSED [ 46%] test/integration/test_scripts.py::TestFigureScripts::test_figure_script_dialog[SplitView] PASSED [ 46%] test/integration/test_scripts.py::TestFigureScripts::test_figure_script_dialog[Thumbnail] PASSED [ 46%] test/integration/test_scripts.py::TestFigureScripts::test_figure_script_dialog[MakeMovie] PASSED [ 46%] test/integration/test_show.py::TestShow::test_empty_path PASSED [ 47%] test/integration/test_show.py::TestShow::test_project_legacy_path PASSED [ 47%] test/integration/test_show.py::TestShow::test_projects_legacy_show PASSED [ 47%] test/integration/test_show.py::TestShow::test_project_dataset_legacy_path PASSED [ 47%] test/integration/test_show.py::TestShow::test_project_dataset_image_legacy_path PASSED [ 47%] test/integration/test_show.py::TestShow::test_tag_redirect[1] PASSED [ 48%] test/integration/test_show.py::TestShow::test_tag_redirect[2] PASSED [ 48%] test/integration/test_show.py::TestShow::test_tagset_redirect[1] PASSED [ 48%] test/integration/test_show.py::TestShow::test_tagset_redirect[2] PASSED [ 48%] test/integration/test_show.py::TestShow::test_tag_legacy_path[1] PASSED [ 49%] test/integration/test_show.py::TestShow::test_tag_legacy_path[2] PASSED [ 49%] test/integration/test_show.py::TestShow::test_tagset_tag_legacy_path PASSED [ 49%] test/integration/test_show.py::TestShow::test_image_legacy_path PASSED [ 49%] test/integration/test_show.py::TestShow::test_screen_legacy_path PASSED [ 50%] test/integration/test_show.py::TestShow::test_screen_plate_legacy_path PASSED [ 50%] test/integration/test_show.py::TestShow::test_screen_plate_well_show PASSED [ 50%] test/integration/test_show.py::TestShow::test_screen_plate_run_well_show[0] PASSED [ 50%] test/integration/test_show.py::TestShow::test_screen_plate_run_well_show[1] PASSED [ 50%] test/integration/test_show.py::TestShow::test_project_dataset_image_show PASSED [ 51%] test/integration/test_show.py::TestShow::test_project_dataset_image_roi_show PASSED [ 51%] test/integration/test_show.py::TestShow::test_project_by_id PASSED [ 51%] test/integration/test_show.py::TestShow::test_project_by_name PASSED [ 51%] test/integration/test_show.py::TestShow::test_tag_by_value[1] PASSED [ 52%] test/integration/test_show.py::TestShow::test_tag_by_value[2] PASSED [ 52%] test/integration/test_show.py::TestShow::test_tagset_tag_by_id PASSED [ 52%] test/integration/test_show.py::TestShow::test_multiple_well_by_id[plate.name=%(plate_name)s|well.name=%(well_name)s-A10] PASSED [ 52%] test/integration/test_show.py::TestShow::test_multiple_well_by_id[plate.name=%(plate_name)s|well.name=%(well_name)s-1J] PASSED [ 52%] test/integration/test_show.py::TestShow::test_screen_plate_run_well_by_name[plate.name=%(plate_name)s|well.name=%(well_name)s-A10] PASSED [ 53%] test/integration/test_show.py::TestShow::test_screen_plate_run_well_by_name[plate.name=%(plate_name)s|well.name=%(well_name)s-1J] PASSED [ 53%] test/integration/test_show.py::TestShow::test_multiple_well_by_id[run=%(plate_acquisition_id)s|well.name=%(well_name)s-A10] PASSED [ 53%] test/integration/test_show.py::TestShow::test_multiple_well_by_id[run=%(plate_acquisition_id)s|well.name=%(well_name)s-1J] PASSED [ 53%] test/integration/test_show.py::TestShow::test_screen_plate_run_well_by_name[run=%(plate_acquisition_id)s|well.name=%(well_name)s-A10] PASSED [ 54%] test/integration/test_show.py::TestShow::test_screen_plate_run_well_by_name[run=%(plate_acquisition_id)s|well.name=%(well_name)s-1J] PASSED [ 54%] test/integration/test_show.py::TestShow::test_well_by_name[A10] PASSED [ 54%] test/integration/test_show.py::TestShow::test_well_by_name[1J] PASSED [ 54%] test/integration/test_show.py::TestShow::test_screen_plate_run_illegal_run PASSED [ 55%] test/integration/test_show.py::TestShow::test_path_to_no_objects PASSED [ 55%] test/integration/test_show.py::TestShow::test_project_dataset_image PASSED [ 55%] test/integration/test_show.py::TestShow::test_project_dataset_images_pagination PASSED [ 55%] test/integration/test_show.py::TestShow::test_orphaned_pagination PASSED [ 55%] test/integration/test_show.py::TestShow::test_get_image_ids_dataset PASSED [ 56%] test/integration/test_show.py::TestShow::test_image PASSED [ 56%] test/integration/test_show.py::TestShow::test_roi PASSED [ 56%] test/integration/test_show.py::TestShow::test_shape PASSED [ 56%] test/integration/test_show.py::TestShow::test_well_image_shape PASSED [ 57%] test/integration/test_show.py::TestShow::test_image_orphan PASSED [ 57%] test/integration/test_show.py::TestShow::test_image_multi_link PASSED [ 57%] test/integration/test_show.py::TestShow::test_image_multi_link_restrict_dataset PASSED [ 57%] test/integration/test_show.py::TestShow::test_image_multi_link_restrict_dataset_project PASSED [ 57%] test/integration/test_show.py::TestShow::test_image_multi_link_restrict_project PASSED [ 58%] test/integration/test_show.py::TestShow::test_dataset PASSED [ 58%] test/integration/test_show.py::TestShow::test_dataset_multi_link PASSED [ 58%] test/integration/test_show.py::TestShow::test_dataset_multi_link_restrict_project PASSED [ 58%] test/integration/test_show.py::TestShow::test_dataset_orphan PASSED [ 59%] test/integration/test_show.py::TestShow::test_project PASSED [ 59%] test/integration/test_show.py::TestShow::test_acquisition PASSED [ 59%] test/integration/test_show.py::TestShow::test_acquisition_restrict_plate PASSED [ 59%] test/integration/test_show.py::TestShow::test_acquisition_restrict_screen PASSED [ 60%] test/integration/test_show.py::TestShow::test_acquisition_restrict_plate_screen PASSED [ 60%] test/integration/test_show.py::TestShow::test_well PASSED [ 60%] test/integration/test_show.py::TestShow::test_well_multi PASSED [ 60%] test/integration/test_show.py::TestShow::test_well_image PASSED [ 60%] test/integration/test_show.py::TestShow::test_well_restrict_acquisition_multi PASSED [ 61%] test/integration/test_show.py::TestShow::test_well_restrict_plate_multi PASSED [ 61%] test/integration/test_show.py::TestShow::test_well_restrict_screen_multi PASSED [ 61%] test/integration/test_show.py::TestShow::test_well_restrict_acquisition_plate_multi PASSED [ 61%] test/integration/test_show.py::TestShow::test_well_restrict_acquisition_screen_multi PASSED [ 62%] test/integration/test_show.py::TestShow::test_well_restrict_acquisition_plate_screen_multi PASSED [ 62%] test/integration/test_show.py::TestShow::test_well_restrict_plate_screen_multi PASSED [ 62%] test/integration/test_show.py::TestShow::test_plate PASSED [ 62%] test/integration/test_show.py::TestShow::test_plate_restrict_screen PASSED [ 62%] test/integration/test_show.py::TestShow::test_screen PASSED [ 63%] test/integration/test_simple.py::TestSimple::testCurrentUser PASSED [ 63%] test/integration/test_simple.py::TestSimple::testImport PASSED [ 63%] test/integration/test_table.py::TestOmeroTables::test_table_html PASSED [ 63%] test/integration/test_table.py::TestOmeroTables::test_table_pagination PASSED [ 64%] test/integration/test_table.py::TestOmeroTables::test_table_query PASSED [ 64%] test/integration/test_table.py::TestOmeroTables::test_table_bitmask[query_result0] PASSED [ 64%] test/integration/test_table.py::TestOmeroTables::test_table_bitmask[query_result1] PASSED [ 64%] test/integration/test_table.py::TestOmeroTables::test_table_bitmask[query_result2] PASSED [ 65%] test/integration/test_table.py::TestOmeroTables::test_table_bitmask[query_result3] PASSED [ 65%] test/integration/test_table.py::TestOmeroTables::test_table_bitmask[query_result4] PASSED [ 65%] test/integration/test_table.py::TestOmeroTables::test_table_bitmask[query_result5] PASSED [ 65%] test/integration/test_table.py::TestOmeroTables::test_table_metadata PASSED [ 65%] test/integration/test_table.py::TestOmeroTables::test_table_get_where_list[query_result0] PASSED [ 66%] test/integration/test_table.py::TestOmeroTables::test_table_get_where_list[query_result1] PASSED [ 66%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice[query_result0] PASSED [ 66%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice[query_result1] PASSED [ 66%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice[query_result2] PASSED [ 67%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice_errors[query_validity0] PASSED [ 67%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice_errors[query_validity1] PASSED [ 67%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice_errors[query_validity2] PASSED [ 67%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice_errors[query_validity3] PASSED [ 67%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice_errors[query_validity4] PASSED [ 68%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice_errors[query_validity5] PASSED [ 68%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice_errors[query_validity6] PASSED [ 68%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice_errors[query_validity7] PASSED [ 68%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice_errors[query_validity8] PASSED [ 69%] test/integration/test_table.py::TestOmeroTables::test_table_perform_slice_errors[query_validity9] PASSED [ 69%] test/integration/test_tags.py::TestTags::test_create_tag_and_tagset PASSED [ 69%] test/integration/test_tags.py::TestTags::test_edit_tag_and_tagset[tagset] PASSED [ 69%] test/integration/test_tags.py::TestTags::test_edit_tag_and_tagset[tag] PASSED [ 70%] test/integration/test_tags.py::TestTags::test_add_edit_and_remove_tag PASSED [ 70%] test/integration/test_tags.py::TestTags::test_add_remove_tags PASSED [ 70%] test/integration/test_thumbnails.py::TestThumbnails::test_default_thumb_size[None] PASSED [ 70%] test/integration/test_thumbnails.py::TestThumbnails::test_default_thumb_size[100] PASSED [ 70%] test/integration/test_thumbnails.py::TestThumbnails::test_base64_thumb[None] PASSED [ 71%] test/integration/test_thumbnails.py::TestThumbnails::test_base64_thumb[100] PASSED [ 71%] test/integration/test_thumbnails.py::TestThumbnails::test_base64_thumb_set PASSED [ 71%] test/integration/test_thumbnails.py::TestRoiThumbnails::test_roi_thumbnail[0-1] PASSED [ 71%] test/integration/test_thumbnails.py::TestRoiThumbnails::test_roi_thumbnail[0-0] PASSED [ 72%] test/integration/test_thumbnails.py::TestRoiThumbnails::test_roi_thumbnail[1-1] PASSED [ 72%] test/integration/test_thumbnails.py::TestRoiThumbnails::test_roi_thumbnail[1-0] PASSED [ 72%] test/integration/test_tree.py::TestTree::test_marshal_experimenter PASSED [ 72%] test/integration/test_tree.py::TestTree::test_marshal_projects_no_results PASSED [ 72%] test/integration/test_tree.py::TestTree::test_marshal_projects_user PASSED [ 73%] test/integration/test_tree.py::TestTree::test_marshal_projects_another_user PASSED [ 73%] test/integration/test_tree.py::TestTree::test_marshal_projects_another_group PASSED [ 73%] test/integration/test_tree.py::TestTree::test_marshal_projects_all_groups PASSED [ 73%] test/integration/test_tree.py::TestTree::test_marshal_projects_all_users PASSED [ 74%] test/integration/test_tree.py::TestTree::test_marshal_projects_all_groups_all_users PASSED [ 74%] test/integration/test_tree.py::TestTree::test_marshal_datasets_no_results PASSED [ 74%] test/integration/test_tree.py::TestTree::test_marshal_datasets_user PASSED [ 74%] test/integration/test_tree.py::TestTree::test_marshal_datasets_another_user PASSED [ 75%] test/integration/test_tree.py::TestTree::test_marshal_datasets_another_group PASSED [ 75%] test/integration/test_tree.py::TestTree::test_marshal_datasets_all_groups PASSED [ 75%] test/integration/test_tree.py::TestTree::test_marshal_datasets_all_users PASSED [ 75%] test/integration/test_tree.py::TestTree::test_marshal_datasets_all_groups_all_users PASSED [ 75%] test/integration/test_tree.py::TestTree::test_marshal_datasets_project PASSED [ 76%] test/integration/test_tree.py::TestTree::test_marshal_datasets_project_crosslink PASSED [ 76%] test/integration/test_tree.py::TestTree::test_marshal_images_no_results PASSED [ 76%] test/integration/test_tree.py::TestTree::test_marshal_images_user PASSED [ 76%] test/integration/test_tree.py::TestTree::test_marshal_images_user_pixels PASSED [ 77%] test/integration/test_tree.py::TestTree::test_marshal_images_thumb_version[thumb0] PASSED [ 77%] test/integration/test_tree.py::TestTree::test_marshal_images_thumb_version[thumb1] PASSED [ 77%] test/integration/test_tree.py::TestTree::test_marshal_images_another_user PASSED [ 77%] test/integration/test_tree.py::TestTree::test_marshal_images_another_group PASSED [ 77%] test/integration/test_tree.py::TestTree::test_marshal_images_all_groups PASSED [ 78%] test/integration/test_tree.py::TestTree::test_marshal_images_all_users PASSED [ 78%] test/integration/test_tree.py::TestTree::test_marshal_images_all_groups_all_users PASSED [ 78%] test/integration/test_tree.py::TestTree::test_marshal_images_dataset PASSED [ 78%] test/integration/test_tree.py::TestTree::test_marshal_images_dataset_no_pixels PASSED [ 79%] test/integration/test_tree.py::TestTree::test_marshal_images_dataset_date PASSED [ 79%] test/integration/test_tree.py::TestTree::test_marshal_images_dataset_crosslink PASSED [ 79%] test/integration/test_tree.py::TestTree::test_marshal_images_share PASSED [ 79%] test/integration/test_tree.py::TestTree::test_marshal_screens_no_results PASSED [ 80%] test/integration/test_tree.py::TestTree::test_marshal_screens_user PASSED [ 80%] test/integration/test_tree.py::TestTree::test_marshal_screens_another_user PASSED [ 80%] test/integration/test_tree.py::TestTree::test_marshal_screens_another_group PASSED [ 80%] test/integration/test_tree.py::TestTree::test_marshal_screens_all_groups PASSED [ 80%] test/integration/test_tree.py::TestTree::test_marshal_screens_all_users PASSED [ 81%] test/integration/test_tree.py::TestTree::test_marshal_screens_all_groups_all_users PASSED [ 81%] test/integration/test_tree.py::TestTree::test_marshal_plates_no_results PASSED [ 81%] test/integration/test_tree.py::TestTree::test_marshal_plates_user PASSED [ 81%] test/integration/test_tree.py::TestTree::test_marshal_plates_another_user PASSED [ 82%] test/integration/test_tree.py::TestTree::test_marshal_plates_another_group PASSED [ 82%] test/integration/test_tree.py::TestTree::test_marshal_plates_all_groups PASSED [ 82%] test/integration/test_tree.py::TestTree::test_marshal_plates_all_users PASSED [ 82%] test/integration/test_tree.py::TestTree::test_marshal_plates_all_groups_all_users PASSED [ 82%] test/integration/test_tree.py::TestTree::test_marshal_plate_acquisitions_no_results PASSED [ 83%] test/integration/test_tree.py::TestTree::test_marshal_plate_acquisitions_user PASSED [ 83%] test/integration/test_tree.py::TestTree::test_marshal_plate_acquisitions_another_user PASSED [ 83%] test/integration/test_tree.py::TestTree::test_marshal_plate_acquisitions_another_group PASSED [ 83%] test/integration/test_tree.py::TestTree::test_marshal_orphaned_no_results PASSED [ 84%] test/integration/test_tree.py::TestTree::test_marshal_orphaned PASSED [ 84%] test/integration/test_tree.py::TestTree::test_marshal_orphaned_another_user PASSED [ 84%] test/integration/test_tree.py::TestTree::test_marshal_orphaned_another_group PASSED [ 84%] test/integration/test_tree.py::TestTree::test_marshal_orphaned_all_groups PASSED [ 85%] test/integration/test_tree.py::TestTree::test_marshal_tags_no_results PASSED [ 85%] test/integration/test_tree.py::TestTree::test_marshal_tags_user PASSED [ 85%] test/integration/test_tree.py::TestTree::test_marshal_tags_another_user PASSED [ 85%] test/integration/test_tree.py::TestTree::test_marshal_tags_another_group PASSED [ 85%] test/integration/test_tree.py::TestTree::test_marshal_tags_all_groups PASSED [ 86%] test/integration/test_tree.py::TestTree::test_marshal_tags_all_users PASSED [ 86%] test/integration/test_tree.py::TestTree::test_marshal_tags_all_groups_all_users PASSED [ 86%] test/integration/test_tree.py::TestTree::test_marshal_tags_orphaned PASSED [ 86%] test/integration/test_tree.py::TestTree::test_marshal_tags_tagset PASSED [ 87%] test/integration/test_tree.py::TestTree::test_marshal_tagged_no_results PASSED [ 87%] test/integration/test_tree.py::TestTree::test_marshal_tagged_user PASSED [ 87%] test/integration/test_tree.py::TestTree::test_marshal_tagged_perms PASSED [ 87%] test/integration/test_tree.py::TestTree::test_marshal_tagged_image_pixels PASSED [ 87%] test/integration/test_tree.py::TestTree::test_marshal_shares_user PASSED [ 88%] test/integration/test_tree.py::TestTree::test_marshal_shares_another_user PASSED [ 88%] test/integration/test_tree.py::TestTree::test_marshal_shares_user_owned PASSED [ 88%] test/integration/test_tree.py::TestTree::test_marshal_shares_another_user_owned PASSED [ 88%] test/integration/test_tree.py::TestTree::test_marshal_discussions_user PASSED [ 89%] test/integration/test_tree.py::TestTree::test_marshal_discussions_another_user PASSED [ 89%] test/integration/test_tree.py::TestTree::test_marshal_discussions_user_owned PASSED [ 89%] test/integration/test_tree.py::TestTree::test_marshal_discussions_another_user_owned PASSED [ 89%] test/integration/test_tree_annotations.py::TestTreeAnnotations::test_single_tag PASSED [ 90%] test/integration/test_tree_annotations.py::TestTreeAnnotations::test_single_tag_userB PASSED [ 90%] test/integration/test_tree_annotations.py::TestTreeAnnotations::test_twin_tags_userA_userB PASSED [ 90%] test/integration/test_tree_annotations.py::TestTreeAnnotations::test_twin_tags_projects PASSED [ 90%] test/integration/test_tree_annotations.py::TestTreeAnnotations::test_tags_comments_project PASSED [ 90%] test/integration/test_tree_annotations.py::TestTreeAnnotations::test_filter_by_namespace PASSED [ 91%] test/integration/test_webadmin.py::TestUserSettings::test_user_settings_page PASSED [ 91%] test/integration/test_webadmin.py::TestUserSettings::test_edit_settings PASSED [ 91%] test/integration/test_webadmin.py::TestExperimenters::test_create_experimenter_roles[user] PASSED [ 91%] test/integration/test_webadmin.py::TestExperimenters::test_create_experimenter_roles[restricted_administrator] PASSED [ 92%] test/integration/test_webadmin.py::TestExperimenters::test_create_experimenter_roles[administrator] PASSED [ 92%] test/integration/test_webadmin.py::TestExperimenters::test_required_fields[required_field0] PASSED [ 92%] test/integration/test_webadmin.py::TestExperimenters::test_required_fields[required_field1] PASSED [ 92%] test/integration/test_webadmin.py::TestExperimenters::test_required_fields[required_field2] PASSED [ 92%] test/integration/test_webadmin.py::TestExperimenters::test_required_fields[required_field3] PASSED [ 93%] test/integration/test_webadmin.py::TestExperimenters::test_required_fields[required_field4] PASSED [ 93%] test/integration/test_webadmin.py::TestExperimenters::test_required_fields[required_field5] PASSED [ 93%] test/integration/test_webadmin.py::TestExperimenters::test_required_fields[required_field6] PASSED [ 93%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin[privilege0] PASSED [ 94%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin[privilege1] PASSED [ 94%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin[privilege2] PASSED [ 94%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin[privilege3] PASSED [ 94%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin[privilege4] PASSED [ 95%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin[privilege5] PASSED [ 95%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin[privilege6] PASSED [ 95%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin[privilege7] PASSED [ 95%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin[privilege8] PASSED [ 95%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin[privilege9] PASSED [ 96%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin_form[privileges0] PASSED [ 96%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin_form[privileges1] PASSED [ 96%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin_form[privileges2] PASSED [ 96%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin_form[privileges3] PASSED [ 97%] test/integration/test_webadmin.py::TestExperimenters::test_create_restricted_admin_form[privileges4] PASSED [ 97%] test/integration/test_webadmin.py::TestExperimenters::test_restricted_admin_create_edit_user PASSED [ 97%] test/integration/test_webadmin.py::TestGroups::test_new_group_form[privileges0] PASSED [ 97%] test/integration/test_webadmin.py::TestGroups::test_new_group_form[privileges1] PASSED [ 97%] test/integration/test_webadmin.py::TestGroups::test_new_group_form[privileges2] PASSED [ 98%] test/integration/test_webadmin.py::TestGroups::test_create_group_permissions[permissions0] PASSED [ 98%] test/integration/test_webadmin.py::TestGroups::test_create_group_permissions[permissions1] PASSED [ 98%] test/integration/test_webadmin.py::TestGroups::test_create_group_permissions[permissions2] PASSED [ 98%] test/integration/test_webadmin.py::TestGroups::test_create_group_permissions[permissions3] PASSED [ 99%] test/integration/test_webadmin.py::TestGroups::test_required_fields[required_field0] PASSED [ 99%] test/integration/test_webadmin.py::TestGroups::test_required_fields[required_field1] PASSED [ 99%] test/integration/test_webadmin.py::TestGroups::test_validation_errors PASSED [ 99%] test/integration/test_webadmin.py::TestGroups::test_save_experimenter PASSED [100%] =============================== warnings summary =============================== OmeroWeb/test/integration/test_annotate.py: 15 warnings OmeroWeb/test/integration/test_api_containers.py: 28 warnings OmeroWeb/test/integration/test_api_errors.py: 4 warnings OmeroWeb/test/integration/test_api_experimenters_groups.py: 12 warnings OmeroWeb/test/integration/test_api_images.py: 3 warnings OmeroWeb/test/integration/test_api_login.py: 4 warnings OmeroWeb/test/integration/test_api_projects.py: 15 warnings OmeroWeb/test/integration/test_api_rois.py: 5 warnings OmeroWeb/test/integration/test_api_wells.py: 5 warnings OmeroWeb/test/integration/test_chgrp.py: 3 warnings OmeroWeb/test/integration/test_chown.py: 3 warnings OmeroWeb/test/integration/test_containers.py: 2 warnings OmeroWeb/test/integration/test_csrf.py: 2 warnings OmeroWeb/test/integration/test_decorators.py: 2 warnings OmeroWeb/test/integration/test_download.py: 4 warnings OmeroWeb/test/integration/test_groups_users.py: 3 warnings OmeroWeb/test/integration/test_histogram.py: 2 warnings OmeroWeb/test/integration/test_history.py: 2 warnings OmeroWeb/test/integration/test_links.py: 2 warnings OmeroWeb/test/integration/test_login.py: 5 warnings OmeroWeb/test/integration/test_marshal.py: 2 warnings OmeroWeb/test/integration/test_metadata.py: 4 warnings OmeroWeb/test/integration/test_plategrid.py: 7 warnings OmeroWeb/test/integration/test_rendering.py: 4 warnings OmeroWeb/test/integration/test_scripts.py: 4 warnings OmeroWeb/test/integration/test_show.py: 2 warnings OmeroWeb/test/integration/test_table.py: 27 warnings OmeroWeb/test/integration/test_tags.py: 2 warnings OmeroWeb/test/integration/test_thumbnails.py: 4 warnings OmeroWeb/test/integration/test_webadmin.py: 18 warnings /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/upgrade_check.py:142: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead self.log.warn("UPGRADE AVAILABLE:" + result) OmeroWeb/test/integration/test_annotate.py: 15 warnings OmeroWeb/test/integration/test_api_containers.py: 28 warnings OmeroWeb/test/integration/test_api_errors.py: 4 warnings OmeroWeb/test/integration/test_api_experimenters_groups.py: 12 warnings OmeroWeb/test/integration/test_api_images.py: 3 warnings OmeroWeb/test/integration/test_api_login.py: 4 warnings OmeroWeb/test/integration/test_api_projects.py: 15 warnings OmeroWeb/test/integration/test_api_rois.py: 5 warnings OmeroWeb/test/integration/test_api_wells.py: 5 warnings OmeroWeb/test/integration/test_chgrp.py: 3 warnings OmeroWeb/test/integration/test_chown.py: 3 warnings OmeroWeb/test/integration/test_containers.py: 2 warnings OmeroWeb/test/integration/test_csrf.py: 2 warnings OmeroWeb/test/integration/test_decorators.py: 2 warnings OmeroWeb/test/integration/test_download.py: 4 warnings OmeroWeb/test/integration/test_groups_users.py: 3 warnings OmeroWeb/test/integration/test_histogram.py: 2 warnings OmeroWeb/test/integration/test_history.py: 2 warnings OmeroWeb/test/integration/test_links.py: 2 warnings OmeroWeb/test/integration/test_login.py: 5 warnings OmeroWeb/test/integration/test_marshal.py: 2 warnings OmeroWeb/test/integration/test_metadata.py: 4 warnings OmeroWeb/test/integration/test_plategrid.py: 7 warnings OmeroWeb/test/integration/test_rendering.py: 4 warnings OmeroWeb/test/integration/test_scripts.py: 4 warnings OmeroWeb/test/integration/test_show.py: 2 warnings OmeroWeb/test/integration/test_table.py: 27 warnings OmeroWeb/test/integration/test_tags.py: 2 warnings OmeroWeb/test/integration/test_thumbnails.py: 4 warnings OmeroWeb/test/integration/test_webadmin.py: 18 warnings /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omeroweb/webadmin/webadmin_utils.py:26: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead logger.warn( OmeroWeb/test/integration/test_annotate.py: 4 warnings OmeroWeb/test/integration/test_api_containers.py: 3 warnings OmeroWeb/test/integration/test_api_projects.py: 1 warning OmeroWeb/test/integration/test_api_rois.py: 1 warning OmeroWeb/test/integration/test_containers.py: 1 warning OmeroWeb/test/integration/test_csrf.py: 3 warnings OmeroWeb/test/integration/test_links.py: 2 warnings OmeroWeb/test/integration/test_show.py: 1 warning OmeroWeb/test/integration/test_tags.py: 11 warnings /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/callbacks.py:270: DeprecationWarning: isSet() is deprecated, use is_set() instead return self.event.isSet() OmeroWeb/test/integration/test_api_errors.py::TestErrors::test_marshal_type /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_marshal/__init__.py:44: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead logger.warn('Requested unknown decoder %s' % t, exc_info=True) OmeroWeb/test/integration/test_api_errors.py::TestErrors::test_marshal_validation /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_marshal/__init__.py:97: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead logger.warn('Requested unknown decoder %s' % t, exc_info=True) OmeroWeb/test/integration/test_api_errors.py::TestErrors::test_security_violation OmeroWeb/test/integration/test_api_errors.py::TestErrors::test_validation_exception OmeroWeb/test/integration/test_api_errors.py::TestErrors::test_project_validation OmeroWeb/test/integration/test_api_projects.py::TestProjects::test_project_delete OmeroWeb/test/integration/test_api_rois.py::TestContainers::test_roi_delete OmeroWeb/test/integration/test_links.py::TestLinks::test_link_datasets_images OmeroWeb/test/integration/test_links.py::TestLinks::test_link_datasets_images /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py:4855: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead logger.warn("%s on %s to <%s> %s(%r, %r)", OmeroWeb/test/integration/test_metadata.py::TestCoreMetadata::test_pixel_size_units OmeroWeb/test/integration/test_metadata.py::TestCoreMetadata::test_pixel_size_units OmeroWeb/test/integration/test_metadata.py::TestCoreMetadata::test_pixel_size_units OmeroWeb/test/integration/test_metadata.py::TestCoreMetadata::test_pixel_size_units OmeroWeb/test/integration/test_metadata.py::TestCoreMetadata::test_none_pixel_size OmeroWeb/test/integration/test_metadata.py::TestCoreMetadata::test_none_pixel_size /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py:1356: DeprecationWarning: Deprecated in OMERO.py 5.22.0. Use getDetails().getExternalInfo(). warnings.warn( OmeroWeb/test/integration/test_metadata.py::TestBulkAnnotations::test_nsbulkannotations_file[True] OmeroWeb/test/integration/test_metadata.py::TestBulkAnnotations::test_nsbulkannotations_file[False] OmeroWeb/test/integration/test_metadata.py::TestBulkAnnotations::test_nsbulkannotations_not_file /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omeroweb/testlib/__init__.py:478: DeprecationWarning: This method is deprecated as of OMERO 5.4.0. Use get warnings.warn( OmeroWeb/test/integration/test_rendering.py::TestRendering::test_copy_past_rendering_settings_from_url OmeroWeb/test/integration/test_rendering.py::TestRendering::test_copy_past_rendering_settings_from_url OmeroWeb/test/integration/test_rendering.py::TestRendering::test_copy_past_rendering_settings_from_url OmeroWeb/test/integration/test_rendering.py::TestRenderImageRegion::test_render_image_region_incomplete_request /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py:8935: DeprecationWarning: setActiveChannels() is deprecated in OMERO 5.4.0.Use set_active_channels warnings.warn("setActiveChannels() is deprecated in OMERO 5.4.0." OmeroWeb/test/integration/test_rendering.py::TestRendering::test_copy_past_rendering_settings_from_url OmeroWeb/test/integration/test_rendering.py::TestRendering::test_copy_past_rendering_settings_from_url OmeroWeb/test/integration/test_rendering.py::TestRendering::test_copy_past_rendering_settings_from_url OmeroWeb/test/integration/test_rendering.py::TestRendering::test_copy_past_rendering_settings_from_url /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py:9197: DeprecationWarning: Deprecated in 5.4.0. Use setChannelInverted() warnings.warn("Deprecated in 5.4.0. Use setChannelInverted()", OmeroWeb/test/integration/test_scripts.py::TestScripts::test_script_inputs_outputs[inputs0] OmeroWeb/test/integration/test_scripts.py::TestScripts::test_script_inputs_outputs[inputs0] OmeroWeb/test/integration/test_scripts.py::TestScripts::test_script_inputs_outputs[inputs1] OmeroWeb/test/integration/test_scripts.py::TestScripts::test_script_inputs_outputs[inputs1] OmeroWeb/test/integration/test_scripts.py::TestScripts::test_script_inputs_outputs[inputs2] OmeroWeb/test/integration/test_scripts.py::TestScripts::test_script_inputs_outputs[inputs2] /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/callbacks.py:89: DeprecationWarning: isSet() is deprecated, use is_set() instead if self.event.isSet(): -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html - generated xml file: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroWeb/target/reports/integration/junit-results.xml - ================ 440 passed, 449 warnings in 1319.24s (0:21:59) ================ !! 12/09/25 03:40:08.234 error: 8 communicators not destroyed during global destruction. BUILD SUCCESSFUL Total time: 22 minutes 1 second + /home/omero/workspace/OMERO-test-integration/src/build.py -f components/tools/OmeroPy/build.xml integration -DMARK=broken -Dtestreports.dir=target/reports/broken Buildfile: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/build.xml Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy... Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy... python-integration: Created dir: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/target/reports/broken ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-9.0.2, pluggy-1.6.0 -- /home/omero/workspace/OMERO-test-integration/.venv3/bin/python3.11 cachedir: .pytest_cache django: version: 5.2.9, settings: omeroweb.settings (from ini) rootdir: /home/omero/workspace/OMERO-test-integration/src/components/tools configfile: pytest.ini plugins: xdist-3.8.0, mock-3.15.1, django-4.11.1 collecting ... collected 2044 items / 2008 deselected / 36 selected test/integration/clitest/test_fs.py::TestFS::testRenameAdminOnly FAILED [ 2%] test/integration/clitest/test_import.py::TestImport::testTargetInDifferentGroup[Dataset-test.fake--d] FAILED [ 5%] test/integration/clitest/test_import.py::TestImport::testTargetInDifferentGroup[Screen-SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake--r] FAILED [ 8%] test/integration/gatewaytest/test_multi_group.py::TestHistory::testCreateHistory FAILED [ 11%] test/integration/gatewaytest/test_multi_group.py::TestScript::testRunScript FAILED [ 13%] test/integration/gatewaytest/test_performance.py::TestPerformance::testListFileAnnotations FAILED [ 16%] test/integration/gatewaytest/test_user.py::TestUser::testCrossGroupRead FAILED [ 19%] test/integration/scriptstest/test_ping.py::TestPing::testProcessCallback FAILED [ 22%] test/integration/scriptstest/test_repo.py::TestScriptRepo::testGetGroupScripts FAILED [ 25%] test/integration/tablestest/test_service.py::TestTables::test2098 FAILED [ 27%] test/integration/tablestest/test_service.py::TestTables::testReadOnlyFile FAILED [ 30%] test/integration/tablestest/test_service.py::TestTables::testReadEqual FAILED [ 33%] test/integration/tablestest/test_service.py::TestTables::testReadOutOfRange FAILED [ 36%] test/integration/test_admin.py::TestAdmin::testChangePasswordWhenUnset FAILED [ 38%] test/integration/test_admin.py::TestAdmin::test9193 FAILED [ 41%] test/integration/test_files.py::TestFiles::testUploadDifferentSizeTicket2337 FAILED [ 44%] test/integration/test_ishare.py::TestIShare::test1172 FAILED [ 47%] test/integration/test_itimeline.py::TestITimeline::test1225 FAILED [ 50%] test/integration/test_permissions.py::TestPermissions::test3136 FAILED [ 52%] test/integration/test_permissions.py::TestPermissions::testSaveWithNegOneExplicit FAILED [ 55%] test/integration/test_permissions.py::TestPermissions::testSaveWithNegBadLink FAILED [ 58%] test/integration/test_permissions.py::TestPermissions::testSaveBadLink FAILED [ 61%] test/integration/test_permissions.py::TestPermissions::testUseOfRawFileBeanScriptReadCorrectGroupAndUser FAILED [ 63%] test/integration/test_rawfilestore.py::TestRFS::testTicket1961Basic FAILED [ 66%] test/integration/test_rawfilestore.py::TestRFS::testTicket1961WithKillSession FAILED [ 69%] test/integration/test_rawfilestore.py::TestRFS::testTicket2161Save FAILED [ 72%] test/integration/test_rawfilestore.py::TestRFS::testNoWrite FAILED [ 75%] test/integration/test_reporawfilestore.py::TestRepoRawFileStore::testFailedWriteNoFile FAILED [ 77%] test/integration/test_scripts.py::TestScripts::testParseErrorTicket2185 PASSED [ 80%] test/integration/test_scripts.py::TestScripts::testAutoFillTicket2326 FAILED [ 83%] test/integration/test_scripts.py::TestScripts::testParamLoadingPerformanceTicket2285 FAILED [ 86%] test/integration/test_scripts.py::TestScripts::test3527 FAILED [ 88%] test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testPrivate10618RootWithNoCtx FAILED [ 91%] test/integration/test_tickets2000.py::TestTickets2000::test1184 FAILED [ 94%] test/integration/test_tickets4000.py::TestTickets4000::test3138 PASSED [ 97%] test/integration/test_tickets6000.py::TestTickets6000::test5684 PASSED [100%] =================================== FAILURES =================================== __________________________ TestFS.testRenameAdminOnly __________________________ self = capsys = <_pytest.capture.CaptureFixture object at 0x7f86de7be8d0> @pytest.mark.broken(reason="fs rename is temporarily disabled") def testRenameAdminOnly(self, capsys): """Test fs rename is admin-only""" self.args += ["rename", "Fileset:1"] with pytest.raises(NonZeroReturnCode): self.cli.invoke(self.args, strict=True) out, err = capsys.readouterr() > assert err.endswith("SecurityViolation: Admins only!\n") E AssertionError: assert False E + where False = ('SecurityViolation: Admins only!\n') E + where = 'disabled since OMERO 5.4.7 due to Pixels.path bug\n'.endswith test/integration/clitest/test_fs.py:118: AssertionError _________ TestImport.testTargetInDifferentGroup[Dataset-test.fake--d] __________ self = container = 'Dataset', filename = 'test.fake', arg = '-d' tmpdir = local('/tmp/pytest-of-omero/pytest-62/testTargetInDifferentGroup_Dat0') capfd = <_pytest.capture.CaptureFixture object at 0x7f86dfc75b10> @pytest.mark.broken(reason="needs omero.group setting") @pytest.mark.parametrize("container,filename,arg", target_fixtures) def testTargetInDifferentGroup(self, container, filename, arg, tmpdir, capfd): new_group = self.new_group(experimenters=[self.user]) self.sf.getAdminService().getEventContext() # Refresh target = eval("omero.model."+container+"I")() target.name = rstring('testTargetInDifferentGroup') target = self.update.saveAndReturnObject( target, {"omero.group": str(new_group.id.val)}) assert target.details.group.id.val == new_group.id.val fakefile = tmpdir.join(filename) fakefile.write('') self.args += [str(fakefile)] self.args += [arg, '%s' % target.id.val] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1216: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 03:40:16,163 242 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 03:40:16,178 257 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 03:40:16,226 305 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 03:40:16,531 610 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 03:40:16,593 672 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 60ms. (63ms total) [0 unknowns] 2025-12-09 03:40:16,626 705 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 03:40:16,984 1063 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 03:40:17,178 1257 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 03:40:17,183 1262 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 03:40:17,184 1263 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 03:40:17,184 1263 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 03:40:17,184 1263 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 03:40:17,184 1263 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 03:40:17,184 1263 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 03:40:17,559 1638 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Dataset:1351 2025-12-09 03:40:17,570 1649 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Could not load target: ome.formats.importer.targets.ModelImportTarget@66a41930 2025-12-09 03:40:17,571 1650 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.RuntimeException: Failed to load target at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:351) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: omero.SecurityViolation: null at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.lang.Class.newInstance(Class.java:584) at IceInternal.BasicStream.createUserException(BasicStream.java:2785) at IceInternal.BasicStream.access$300(BasicStream.java:14) at IceInternal.BasicStream$EncapsDecoder11.throwException(BasicStream.java:3620) at IceInternal.BasicStream.throwException(BasicStream.java:2291) at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399) at omero.api.IQueryPrxHelper.end_get(IQueryPrxHelper.java:2000) at omero.api.IQueryPrxHelper.get(IQueryPrxHelper.java:1872) at omero.api.IQueryPrxHelper.get(IQueryPrxHelper.java:1859) at ome.formats.importer.targets.ModelImportTarget.load(ModelImportTarget.java:219) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:334) ... 7 common frames omitted 2025-12-09 03:40:17,573 1652 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 0 files uploaded, 0 filesets created, 0 images imported, 0 errors in 0:00:00.282 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted _ TestImport.testTargetInDifferentGroup[Screen-SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake--r] _ self = container = 'Screen' filename = 'SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake' arg = '-r' tmpdir = local('/tmp/pytest-of-omero/pytest-62/testTargetInDifferentGroup_Scr0') capfd = <_pytest.capture.CaptureFixture object at 0x7f86e4571cd0> @pytest.mark.broken(reason="needs omero.group setting") @pytest.mark.parametrize("container,filename,arg", target_fixtures) def testTargetInDifferentGroup(self, container, filename, arg, tmpdir, capfd): new_group = self.new_group(experimenters=[self.user]) self.sf.getAdminService().getEventContext() # Refresh target = eval("omero.model."+container+"I")() target.name = rstring('testTargetInDifferentGroup') target = self.update.saveAndReturnObject( target, {"omero.group": str(new_group.id.val)}) assert target.details.group.id.val == new_group.id.val fakefile = tmpdir.join(filename) fakefile.write('') self.args += [str(fakefile)] self.args += [arg, '%s' % target.id.val] # Invoke CLI import command and retrieve stdout/stderr > o, e = self.do_import(capfd) ^^^^^^^^^^^^^^^^^^^^^ test/integration/clitest/test_import.py:1216: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/clitest/test_import.py:150: in do_import self.cli.invoke(self.args, strict=True) ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1211: in invoke self.assertRC() _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def assertRC(self): if self.rv != 0: > raise NonZeroReturnCode(self.rv, "assert failed") E omero.cli.NonZeroReturnCode: assert failed ../../../../.venv3/lib64/python3.11/site-packages/omero/cli.py:1200: NonZeroReturnCode ----------------------------- Captured stdout call ----------------------------- OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 2025-12-09 03:40:18,291 254 [ main] INFO ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.8.4-SNAPSHOT 2025-12-09 03:40:18,306 269 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 8.4.0-SNAPSHOT revision: 26fd5a143365bab40e31a18ef4b27e020715f445 date: 9 December 2025 2025-12-09 03:40:18,355 318 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO 2025-12-09 03:40:18,669 632 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM 2025-12-09 03:40:18,813 776 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 142ms. (145ms total) [0 unknowns] 2025-12-09 03:40:18,847 810 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:14064 2025-12-09 03:40:19,212 1175 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back 2025-12-09 03:40:19,421 1384 [ main] INFO ome.formats.OMEROMetadataStoreClient - Pinging session every 300s. 2025-12-09 03:40:19,426 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.6.3 2025-12-09 03:40:19,426 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.8.4-SNAPSHOT 2025-12-09 03:40:19,426 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.25 2025-12-09 03:40:19,426 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux 2025-12-09 03:40:19,426 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64 2025-12-09 03:40:19,426 1389 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 5.14.0-611.11.1.el9_7.x86_64 2025-12-09 03:40:19,763 1726 [ main] INFO ome.formats.importer.ImportConfig - Using import target: Screen:219 2025-12-09 03:40:19,772 1735 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Could not load target: ome.formats.importer.targets.ModelImportTarget@4e769805 2025-12-09 03:40:19,773 1736 [2-thread-1] ERROR ome.formats.importer.ImportLibrary - Error on import java.lang.RuntimeException: Failed to load target at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:351) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:328) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: omero.SecurityViolation: null at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.lang.Class.newInstance(Class.java:584) at IceInternal.BasicStream.createUserException(BasicStream.java:2785) at IceInternal.BasicStream.access$300(BasicStream.java:14) at IceInternal.BasicStream$EncapsDecoder11.throwException(BasicStream.java:3620) at IceInternal.BasicStream.throwException(BasicStream.java:2291) at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399) at omero.api.IQueryPrxHelper.end_get(IQueryPrxHelper.java:2000) at omero.api.IQueryPrxHelper.get(IQueryPrxHelper.java:1872) at omero.api.IQueryPrxHelper.get(IQueryPrxHelper.java:1859) at ome.formats.importer.targets.ModelImportTarget.load(ModelImportTarget.java:219) at ome.formats.importer.ImportLibrary$1.call(ImportLibrary.java:334) ... 7 common frames omitted 2025-12-09 03:40:19,775 1738 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Exiting on error ==> Summary 0 files uploaded, 0 filesets created, 0 images imported, 0 errors in 0:00:00.256 ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.util.Resources:__init__.py:669 Halted ________________________ TestHistory.testCreateHistory _________________________ self = gatewaywrapper = @pytest.mark.broken(ticket="11494") def testCreateHistory(self, gatewaywrapper): # Login as user... gatewaywrapper.doLogin(dbhelpers.USERS['history_test_user']) userId = gatewaywrapper.gateway.getEventContext().userId uuid = gatewaywrapper.gateway.getEventContext().sessionUuid default_groupId = gatewaywrapper.gateway.getEventContext().groupId start = int(round(time.time() * 1000)) - 1000 # Create Dataset in 'default' group update = gatewaywrapper.gateway.getUpdateService() new_ds = omero.model.DatasetI() dataset_name = "history_test_%s" % uuid new_ds.name = rstring(dataset_name) new_ds = update.saveAndReturnObject(new_ds) new_ds_Id = new_ds.id.val # As Admin, create a second group with this user & upload script gatewaywrapper.loginAsAdmin() gid = gatewaywrapper.gateway.createGroup( "history-test-%s" % uuid, member_Ids=[userId], perms=READWRITE) # login as User gatewaywrapper.doLogin(dbhelpers.USERS['history_test_user']) end = int(round(time.time() * 1000)) + 1000 self.searchHistory(gatewaywrapper.gateway, start, end) # switch user into new group switched = gatewaywrapper.gateway.c.sf.setSecurityContext( omero.model.ExperimenterGroupI(gid, False)) assert switched, "Failed to switch into new group" # Shouldn't be able to access Dataset... > self.searchHistory(gatewaywrapper.gateway, start, end) test/integration/gatewaytest/test_multi_group.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = gateway = start = 1765251620108, end = 1765251622244, dtype = 'Dataset' def searchHistory(self, gateway, start, end, dtype="Dataset"): tm = gateway.getTimelineService() count = tm.countByPeriod([dtype], rtime(int(start)), rtime(int(end)), None, gateway.SERVICE_OPTS) data = tm.getByPeriod([dtype], rtime(int(start)), rtime(int(end)), None, True, gateway.SERVICE_OPTS) logs = tm.getEventLogsByPeriod(rtime(start), rtime(end), None, gateway.SERVICE_OPTS) entityType = 'ome.model.containers.%s' % dtype filteredLogs = [{'id': i.entityId.val, 'action': i.action.val} for i in logs if i.entityType.val == entityType] typeCount = count[dtype] dataCount = len(data[dtype]) logCount = len(filteredLogs) assert typeCount == dataCount, \ "Period count should match number of objects" > assert logCount == dataCount, \ "Logs count should match number of objects" E AssertionError: Logs count should match number of objects E assert 1 == 0 test/integration/gatewaytest/test_multi_group.py:58: AssertionError ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=f25c9784-b6a6-4fb3-a000-3b57004714a1) INFO omero.gateway:__init__.py:2307 created connection (uuid=812134db-c660-43f4-b1c6-8498e7573a3d) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=0989ab35-0af0-48ae-9eea-f501d3e5a8cb) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=ebcc9281-3c92-4b06-9997-898142d29a9a) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=d1de14a2-3fd1-4bff-818b-9af5c23e8efc) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=2666ba6f-f0d6-4903-a314-1f7bf9cdaa38) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=71042c76-858d-466e-a08b-6198f3c69d0e) WARNING omero.gateway:__init__.py:4855 ApiUsageException on to lookupExperimenter(('history_test_user',), {}) Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py", line 4875, in __call__ return self.f(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IAdmin_ice.py", line 824, in lookupExperimenter return _M_omero.api.IAdmin._op_lookupExperimenter.invoke(self, ((name, ), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ApiUsageException: exception ::omero::ApiUsageException { serverStackTrace = ome.conditions.ApiUsageException: No such experimenter: history_test_user at ome.logic.AdminImpl.lookupExperimenter(AdminImpl.java:325) at jdk.internal.reflect.GeneratedMethodAccessor603.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy91.lookupExperimenter(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor603.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy91.lookupExperimenter(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor3293.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) at ome.services.blitz.impl.AdminI.lookupExperimenter_async(AdminI.java:256) at jdk.internal.reflect.GeneratedMethodAccessor3292.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy92.lookupExperimenter_async(Unknown Source) at omero.api._IAdminTie.lookupExperimenter_async(_IAdminTie.java:264) at omero.api._IAdminDisp.___lookupExperimenter(_IAdminDisp.java:924) at omero.api._IAdminDisp.__dispatch(_IAdminDisp.java:2345) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ApiUsageException message = No such experimenter: history_test_user } WARNING omero.gateway:__init__.py:4855 ApiUsageException on to lookupGroup(('rw_history',), {}) Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py", line 4875, in __call__ return self.f(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IAdmin_ice.py", line 937, in lookupGroup return _M_omero.api.IAdmin._op_lookupGroup.invoke(self, ((name, ), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ApiUsageException: exception ::omero::ApiUsageException { serverStackTrace = ome.conditions.ApiUsageException: No such group: rw_history at ome.logic.AdminImpl.lookupGroup(AdminImpl.java:366) at jdk.internal.reflect.GeneratedMethodAccessor483.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy91.lookupGroup(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor483.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy91.lookupGroup(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor537.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) at ome.services.blitz.impl.AdminI.lookupGroup_async(AdminI.java:266) at jdk.internal.reflect.GeneratedMethodAccessor536.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy92.lookupGroup_async(Unknown Source) at omero.api._IAdminTie.lookupGroup_async(_IAdminTie.java:276) at omero.api._IAdminDisp.___lookupGroup(_IAdminDisp.java:990) at omero.api._IAdminDisp.__dispatch(_IAdminDisp.java:2353) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ApiUsageException message = No such group: rw_history } INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ------------------------------ Captured log call ------------------------------- INFO omero.gateway:__init__.py:2307 created connection (uuid=cf7eb3c9-13a1-47e0-b9bb-b7d1413fc151) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=ba07a3d6-4a4f-47e4-bb28-412c50ead7f7) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=ac236046-f83a-411d-bf6d-766d772eed3c) --------------------------- Captured stderr teardown --------------------------- ** ---------------------------- Captured log teardown ----------------------------- INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=8daffc12-f073-40be-83e4-db60a1ddc122) INFO omero.gateway:__init__.py:2307 created connection (uuid=e7093dbb-007d-43ff-8980-1ff78027c846) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=b236b77e-0add-47f3-881e-84ab822a31c1) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ___________________________ TestScript.testRunScript ___________________________ self = gatewaywrapper = @pytest.mark.broken(ticket="11610") def testRunScript(self, gatewaywrapper): # Login as user... gatewaywrapper.doLogin(dbhelpers.USERS['script_test_user']) userId = gatewaywrapper.gateway.getEventContext().userId uuid = gatewaywrapper.gateway.getEventContext().sessionUuid default_groupId = gatewaywrapper.gateway.getEventContext().groupId # Create Dataset in 'default' group update = gatewaywrapper.gateway.getUpdateService() new_ds = omero.model.DatasetI() dataset_name = "script_test_%s" % uuid new_ds.name = rstring(dataset_name) new_ds = update.saveAndReturnObject(new_ds) new_ds_Id = new_ds.id.val # As Admin, create a second group with this user & upload script gatewaywrapper.loginAsAdmin() gid = gatewaywrapper.gateway.createGroup( "script-test-%s" % uuid, member_Ids=[userId], perms=READWRITE) SCRIPT = """if True: import omero.scripts import omero.rtypes client = omero.scripts.client("ticket8573", \ omero.scripts.Long("datasetId"), \ omero.scripts.String("datasetName", out=True)) ec = client.sf.getAdminService().getEventContext() gid = ec.groupId qs = client.sf.getQueryService() ds_Id = client.getInput("datasetId").getValue() print("Running test...") # generate stdout try: dataset = qs.find("Dataset", ds_Id) ds_Name = dataset.name.val print(ds_Name) except Exception: ds_Name = "Not Found" client.setOutput("gid", omero.rtypes.rlong(gid)) client.setOutput("datasetName", omero.rtypes.rstring(ds_Name)) """ svc = gatewaywrapper.gateway.getScriptService() scriptID = svc.uploadOfficialScript( "/test/ticket8573/%s" % uuid, SCRIPT) # switch user into new group gatewaywrapper.doLogin(dbhelpers.USERS['script_test_user']) switched = gatewaywrapper.gateway.c.sf.setSecurityContext( omero.model.ExperimenterGroupI(gid, False)) assert switched, "Failed to switch into new group" # Shouldn't be able to access Dataset... value = gatewaywrapper.gateway.getObject("Dataset", new_ds_Id) assert value is None gatewaywrapper.gateway.SERVICE_OPTS.setOmeroGroup( str(default_groupId)) value = gatewaywrapper.gateway.getObject("Dataset", new_ds_Id) assert value is not None # run script svc = gatewaywrapper.gateway.getScriptService() > process = svc.runScript(scriptID, {"datasetId": rlong(new_ds_Id)}, None, gatewaywrapper.gateway.SERVICE_OPTS) test/integration/gatewaytest/test_multi_group.py:188: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py:4878: in __call__ return self.handle_exception(e, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ../../../../.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py:4875: in __call__ return self.f(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = 319990de-f8f3-4b34-96f1-78d71701e971/8aa3c6b0-efc0-4d57-adc6-14832665c9b4omero.api.IScript -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 scriptID = 6042 inputs = {'datasetId': object #0 (::omero::RLong) { _val = 1359 }} waitSecs = None _ctx = def runScript(self, scriptID, inputs, waitSecs, _ctx=None): > return _M_omero.api.IScript._op_runScript.invoke(self, ((scriptID, inputs, waitSecs), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E omero.NoProcessorAvailable: exception ::omero::NoProcessorAvailable E { E serverStackTrace = E serverExceptionClass = E message = No processor available! [0 response(s)] E processorCount = 0 E } ../../../../.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py:935: NoProcessorAvailable ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=ee53143c-62ac-47b8-ab94-cedfe358c1d7) INFO omero.gateway:__init__.py:2307 created connection (uuid=5e5b8839-360d-4950-b234-490f979cb1a1) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=b7c5ecc8-d1ce-4757-bd50-2294de0e6f5e) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=90fabcb3-0ace-4be3-ae5e-d1c731b74440) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=6f5e26da-0f3a-4a4a-a7ab-b4ec38a79df2) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=8f29e49c-c20b-4325-b15f-261161f76ee4) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=59e85304-5f32-41c7-b7ec-70d29e62267a) WARNING omero.gateway:__init__.py:4855 ApiUsageException on to <52dd9ed4-73eb-4b4c-8e4d-f305789e628bomero.api.IAdmin> lookupExperimenter(('script_test_user',), {}) Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py", line 4875, in __call__ return self.f(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IAdmin_ice.py", line 824, in lookupExperimenter return _M_omero.api.IAdmin._op_lookupExperimenter.invoke(self, ((name, ), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ApiUsageException: exception ::omero::ApiUsageException { serverStackTrace = ome.conditions.ApiUsageException: No such experimenter: script_test_user at ome.logic.AdminImpl.lookupExperimenter(AdminImpl.java:325) at jdk.internal.reflect.GeneratedMethodAccessor603.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy91.lookupExperimenter(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor603.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy91.lookupExperimenter(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor3293.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) at ome.services.blitz.impl.AdminI.lookupExperimenter_async(AdminI.java:256) at jdk.internal.reflect.GeneratedMethodAccessor3292.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy92.lookupExperimenter_async(Unknown Source) at omero.api._IAdminTie.lookupExperimenter_async(_IAdminTie.java:264) at omero.api._IAdminDisp.___lookupExperimenter(_IAdminDisp.java:924) at omero.api._IAdminDisp.__dispatch(_IAdminDisp.java:2345) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ApiUsageException message = No such experimenter: script_test_user } WARNING omero.gateway:__init__.py:4855 ApiUsageException on to <52dd9ed4-73eb-4b4c-8e4d-f305789e628bomero.api.IAdmin> lookupGroup(('rw_script',), {}) Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py", line 4875, in __call__ return self.f(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IAdmin_ice.py", line 937, in lookupGroup return _M_omero.api.IAdmin._op_lookupGroup.invoke(self, ((name, ), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ApiUsageException: exception ::omero::ApiUsageException { serverStackTrace = ome.conditions.ApiUsageException: No such group: rw_script at ome.logic.AdminImpl.lookupGroup(AdminImpl.java:366) at jdk.internal.reflect.GeneratedMethodAccessor483.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy91.lookupGroup(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor483.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy91.lookupGroup(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor537.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) at ome.services.blitz.impl.AdminI.lookupGroup_async(AdminI.java:266) at jdk.internal.reflect.GeneratedMethodAccessor536.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy92.lookupGroup_async(Unknown Source) at omero.api._IAdminTie.lookupGroup_async(_IAdminTie.java:276) at omero.api._IAdminDisp.___lookupGroup(_IAdminDisp.java:990) at omero.api._IAdminDisp.__dispatch(_IAdminDisp.java:2353) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ApiUsageException message = No such group: rw_script } INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ------------------------------ Captured log call ------------------------------- INFO omero.gateway:__init__.py:2307 created connection (uuid=e51736b8-e428-49b4-9ac5-dc5a80834b97) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=ac6d3816-6be0-4e63-9d74-9bb1a3663b8f) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=319990de-f8f3-4b34-96f1-78d71701e971) WARNING omero.gateway:__init__.py:4855 NoProcessorAvailable on to <8aa3c6b0-efc0-4d57-adc6-14832665c9b4omero.api.IScript> runScript((6042, {'datasetId': object #0 (::omero::RLong) { _val = 1359 }}, None, ), {}) Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py", line 4875, in __call__ return self.f(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 935, in runScript return _M_omero.api.IScript._op_runScript.invoke(self, ((scriptID, inputs, waitSecs), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.NoProcessorAvailable: exception ::omero::NoProcessorAvailable { serverStackTrace = serverExceptionClass = message = No processor available! [0 response(s)] processorCount = 0 } --------------------------- Captured stderr teardown --------------------------- ** ---------------------------- Captured log teardown ----------------------------- INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=ff956b1d-abb6-4838-b329-c667f34740a0) INFO omero.gateway:__init__.py:2307 created connection (uuid=46e95491-6657-4319-a2da-bfedf5606dee) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=71a5fbce-e682-4d28-a4e1-6832ec765796) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ___________________ TestPerformance.testListFileAnnotations ____________________ self = gatewaywrapper = @pytest.mark.broken(ticket="11494") def testListFileAnnotations(self, gatewaywrapper): """ testListFileAnnotations: test speed of getObjects('FileAnnotation') vv listFileAnnotations() """ gatewaywrapper.loginAsAuthor() updateService = gatewaywrapper.gateway.getUpdateService() def createFileAnnotation(name, ns): originalFile = omero.model.OriginalFileI() originalFile.setName(rstring(name)) originalFile.setPath(rstring(name)) originalFile.setSize(rlong(0)) originalFile.setHash(rstring("Foo")) originalFile = updateService.saveAndReturnObject(originalFile) fa = omero.model.FileAnnotationI() fa.setFile(originalFile) fa.setNs(rstring(ns)) fa = updateService.saveAndReturnObject(fa) return fa.id.val ns = "omero.gatewaytest.PerformanceTest.testListFileAnnotations" fileCount = 250 fileAnnIds = [createFileAnnotation("testListFileAnnotations%s" % i, ns) for i in range(fileCount)] # test speed of listFileAnnotations startTime = time.time() fileCount = 0 fileAnns = gatewaywrapper.gateway.listFileAnnotations(toInclude=[ns]) for fa in fileAnns: fa.getFileName() fileCount += 1 t1 = time.time() - startTime print("listFileAnnotations for %d files = %s secs" % (fileCount, t1)) # Typically 1.4 secs # test speed of getOjbects("Annotation") - lazy loading file names startTime = time.time() fileCount = 0 fileAnns = gatewaywrapper.gateway.getObjects( "FileAnnotation", attributes={'ns': ns}) for fa in fileAnns: fa.getFileName() fileCount += 1 t2 = time.time() - startTime print("getObjects, lazy loading file names for %d files = %s secs" % (fileCount, t2)) # Typically 2.8 secs # test speed of getOjbects("Annotation") - NO loading file names startTime = time.time() fileCount = 0 fileAnns = gatewaywrapper.gateway.getObjects( "FileAnnotation", attributes={'ns': ns}) for fa in fileAnns: fa.getId() fileCount += 1 t3 = time.time() - startTime print("getObjects, NO file names for %d files = %s secs" % (fileCount, t3)) # Typically 0.4 secs > assert t1 < t2, "Blitz listFileAnnotations() should be faster " \ "than getObjects('FileAnnotation')" E AssertionError: Blitz listFileAnnotations() should be faster than getObjects('FileAnnotation') E assert 0.2187957763671875 < 0.14293193817138672 test/integration/gatewaytest/test_performance.py:91: AssertionError ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=36c5b3c2-8e9e-42d2-957d-a979e6b3231a) INFO omero.gateway:__init__.py:2307 created connection (uuid=27419e21-35d1-4c08-a699-2a4d1a18150a) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=22ec8cbd-be39-4569-8c08-4791ffbc230b) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=8a601857-9341-423e-bd2e-efe9e1690643) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=4e798fd9-206a-4aff-a6d4-5e213376684b) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=a9d2fb6e-9b74-4049-8a9a-0963877d77d8) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ----------------------------- Captured stdout call ----------------------------- listFileAnnotations for 250 files = 0.2187957763671875 secs getObjects, lazy loading file names for 250 files = 0.14293193817138672 secs getObjects, NO file names for 250 files = 0.13431859016418457 secs ------------------------------ Captured log call ------------------------------- INFO omero.gateway:__init__.py:2307 created connection (uuid=6dc5031f-78ae-4ab6-a5fa-3e200575443f) --------------------------- Captured stderr teardown --------------------------- ** ---------------------------- Captured log teardown ----------------------------- INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=74d788fb-6115-44e0-b2f1-407436a6a0dc) INFO omero.gateway:__init__.py:2307 created connection (uuid=297842f6-ed04-40ff-b52a-865c828ab84e) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=530b902e-bcad-4fde-a962-185ba442842c) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _________________________ TestUser.testCrossGroupRead __________________________ self = gatewaywrapper = @pytest.mark.broken(ticket="11545") def testCrossGroupRead(self, gatewaywrapper): gatewaywrapper.loginAsAuthor() p = gatewaywrapper.getTestProject() assert str(p.getDetails().permissions)[4] == '-' d = p.getDetails() g = d.getGroup() gatewaywrapper.loginAsUser() gatewaywrapper.gateway.SERVICE_OPTS.setOmeroGroup('-1') > assert not g.getId() in \ gatewaywrapper.gateway.getEventContext().memberOfGroups E assert not 2719 in [2718, 1, 2730, 2719, 2785] E + where 2719 = getId() E + where getId = <_ExperimenterGroupWrapper id=2719>.getId E + and [2718, 1, 2730, 2719, 2785] = object #0 (::omero::sys::EventContext)\n{\n shareId = -1\n sessionId = 10358\n sessionUuid = b45a39b5-81cc-48e6-945f-05bff89a042d\n userId = 3716\n userName = weblitz_test_user\n sudoerId = \n sudoerName = \n groupId = 2718\n groupName = weblitz_test_user_group\n isAdmin = False\n adminPrivileges = \n {\n }\n eventId = -1\n eventType = Internal\n memberOfGroups = \n {\n [0] = 2718\n [1] = 1\n [2] = 2730\n [3] = 2719\n [4] = 2785\n }\n leaderOfGroups = \n {\n }\n groupPermissions = object #1 (::omero::model::Permissions)\n {\n _restrictions = \n {\n }\n _extendedRestrictions = \n {\n }\n _perm1 = -56\n }\n}.memberOfGroups E + where object #0 (::omero::sys::EventContext)\n{\n shareId = -1\n sessionId = 10358\n sessionUuid = b45a39b5-81cc-48e6-945f-05bff89a042d\n userId = 3716\n userName = weblitz_test_user\n sudoerId = \n sudoerName = \n groupId = 2718\n groupName = weblitz_test_user_group\n isAdmin = False\n adminPrivileges = \n {\n }\n eventId = -1\n eventType = Internal\n memberOfGroups = \n {\n [0] = 2718\n [1] = 1\n [2] = 2730\n [3] = 2719\n [4] = 2785\n }\n leaderOfGroups = \n {\n }\n groupPermissions = object #1 (::omero::model::Permissions)\n {\n _restrictions = \n {\n }\n _extendedRestrictions = \n {\n }\n _perm1 = -56\n }\n} = getEventContext() E + where getEventContext = .getEventContext E + where = .gateway test/integration/gatewaytest/test_user.py:127: AssertionError ------------------------------ Captured log setup ------------------------------ INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=33561971-1873-4cba-84bd-bf9fe7256df4) INFO omero.gateway:__init__.py:2307 created connection (uuid=a9f3274c-bff1-4d9b-b791-2f1662c5bef1) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=ae5cc73c-79af-47f8-805c-9f2193b1674c) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=0ff81380-7874-4dbc-bfa2-e9b977996949) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=e239e33c-4e42-4af6-a67a-2067f37941ba) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=09359f4f-17ed-4ec9-a7f5-7038d3de8fb1) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) ------------------------------ Captured log call ------------------------------- INFO omero.gateway:__init__.py:2307 created connection (uuid=23811246-0dcb-4cb2-bbb4-f2e24ccb2e47) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=b45a39b5-81cc-48e6-945f-05bff89a042d) --------------------------- Captured stderr teardown --------------------------- ** ---------------------------- Captured log teardown ----------------------------- INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=5b245262-72f6-4a37-ac32-c005ea1deb5a) INFO omero.gateway:__init__.py:2307 created connection (uuid=9e211638-c800-4165-a058-c8845323c7d7) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) INFO omero.gateway:__init__.py:2307 created connection (uuid=1a558e7b-95e5-41b3-8a78-a0b667abaf22) INFO omero.gateway:__init__.py:2009 closed connection (uuid=None) _________________________ TestPing.testProcessCallback _________________________ self = @pytest.mark.broken(ticket="11494") def testProcessCallback(self): callback = CallbackI() id = self.client.getCommunicator().stringToIdentity(str(uuid.uuid4())) cb = self.client.getAdapter().add(callback, id) cb = omero.grid.ProcessCallbackPrx.uncheckedCast(cb) p = self._getProcessor() params = p.params() assert params.stdoutFormat process = p.execute(rmap({})) process.registerCallback(cb) self.assertSuccess(p, process) > assert len(callback.finish) > 0 E assert 0 > 0 E + where 0 = len([]) E + where [] = object #0 (::omero::grid::ProcessCallback)\n{\n}.finish test/integration/scriptstest/test_ping.py:214: AssertionError ______________________ TestScriptRepo.testGetGroupScripts ______________________ self = @pytest.mark.broken(ticket="11494") def testGetGroupScripts(self): scriptService = self.sf.getScriptService() client = self.new_client(self.group) sid = client.sf.getScriptService().uploadScript( "/test/otheruser.py", """if True: import omero, omero.scripts as OS OS.client("testGetGroupScripts") """) myGroupScripts = scriptService.getUserScripts( [omero.model.ExperimenterGroupI(self.group.id.val, False)]) > assert sid in [x.id.val for x in myGroupScripts] E assert 6298 in [] test/integration/scriptstest/test_repo.py:78: AssertionError _____________________________ TestTables.test2098 ______________________________ self = @pytest.mark.broken(ticket="11534") def test2098(self): """ Creates and downloads an HDF file and checks that its size and hash match whats in the db """ grid = self.client.sf.sharedResources() table = grid.newTable(1, "/test") assert table lc = columns.LongColumnI('lc', 'desc', [1]) file = None try: file = table.getOriginalFile() assert file table.initialize([lc]) table.addData([lc]) finally: # Not deleting since queried table.close() # Reload the file file = self.client.sf.getQueryService().get( "OriginalFile", file.id.val) # Check values > p = path.path(self.tmpfile()) ^^^^^^^^^ E AttributeError: type object 'path' has no attribute 'path' test/integration/tablestest/test_service.py:154: AttributeError _________________________ TestTables.testReadOnlyFile __________________________ self = @pytest.mark.broken(ticket="unimplemented") def testReadOnlyFile(self): """ Create an HDF5 file on the server, and then mark it read-only. The server should still allow you to load & read that file. """ self.createBlankTable() # ofile > filename = self.unique_dir + "/file.txt" ^^^^^^^^^^^^^^^ E AttributeError: 'TestTables' object has no attribute 'unique_dir' test/integration/tablestest/test_service.py:661: AttributeError ___________________________ TestTables.testReadEqual ___________________________ self = twoColumnFiveRowTable = df2bb0cc-9986-469d-8994-bdbdadc8e32c/Table-ca54b6cb-21f3-483f-bd4e-30593a48fb32 -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 @pytest.mark.broken(reason="start=0,end=0 to be reviewed") def testReadEqual(self, twoColumnFiveRowTable): # start=0, end=0 has a special contract data = twoColumnFiveRowTable.read([0], 0, 0) assert 1 == len(data.columns) > assert [1] == data.columns[0].values E assert [1] == [1, 2, 3, 4, 5] E E Right contains 4 more items, first extra item: 2 E E Full diff: E [ E 1, E - 2, E - 3, E - 4, E - 5, E ] test/integration/tablestest/test_service.py:967: AssertionError ________________________ TestTables.testReadOutOfRange _________________________ self = twoColumnFiveRowTable = df2bb0cc-9986-469d-8994-bdbdadc8e32c/Table-9205f95a-f722-4fe6-b45b-9d42a263bbe1 -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 @pytest.mark.broken(reason="need to be reviewed") def testReadOutOfRange(self, twoColumnFiveRowTable): # [1, 2, 3, 4, 5][-1:5] = [5] data = twoColumnFiveRowTable.read([0], -1, 5) assert 1 == len(data.columns) assert [5] == data.columns[0].values > assert [4] == data.rowNumbers E assert [4] == [-1, 0, 1, 2, 3, 4] E E At index 0 diff: 4 != -1 E Right contains 5 more items, first extra item: 0 E E Full diff: E [ E - -1, E - 0, E - 1, E - 2, E - 3, E 4, E ] test/integration/tablestest/test_service.py:1015: AssertionError ____________________ TestAdmin.testChangePasswordWhenUnset _____________________ self = @pytest.mark.broken(reason="Empty password disabled by config", ticket="3201") def testChangePasswordWhenUnset(self): """ Shows that it's possible to use the changePasswordWithOldPassword when previously no password was set. See ticket:3201 """ client = self.new_client() admin = client.sf.getAdminService() # By setting the user's password to the empty string # any password will be allowed as the old password admin.changePassword(rstring("")) > admin.changePasswordWithOldPassword(rstring("IGNORED"), rstring("ome")) test/integration/test_admin.py:118: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = 47c528bd-097f-4b8d-ada0-33eedcbccbb9/4a593c15-0e5e-4331-a795-faf8d42847bbomero.api.IAdmin -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 oldPassword = object #0 (::omero::RString) { _val = IGNORED } newPassword = object #0 (::omero::RString) { _val = ome }, _ctx = None def changePasswordWithOldPassword(self, oldPassword, newPassword, _ctx=None): > return _M_omero.api.IAdmin._op_changePasswordWithOldPassword.invoke(self, ((oldPassword, newPassword), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E omero.SecurityViolation: exception ::omero::SecurityViolation E { E serverStackTrace = ome.conditions.SecurityViolation: Old password is invalid E at ome.logic.AdminImpl.changePasswordWithOldPassword(AdminImpl.java:1253) E at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) E at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.EventHandler.invoke(EventHandler.java:154) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) E at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) E at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy91.changePasswordWithOldPassword(Unknown Source) E at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) E at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy91.changePasswordWithOldPassword(Unknown Source) E at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) E at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) E at ome.services.throttling.Callback.run(Callback.java:56) E at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) E at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) E at ome.services.blitz.impl.AdminI.changePasswordWithOldPassword_async(AdminI.java:144) E at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) E at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at omero.cmd.CallContext.invoke(CallContext.java:85) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy92.changePasswordWithOldPassword_async(Unknown Source) E at omero.api._IAdminTie.changePasswordWithOldPassword_async(_IAdminTie.java:112) E at omero.api._IAdminDisp.___changePasswordWithOldPassword(_IAdminDisp.java:1977) E at omero.api._IAdminDisp.__dispatch(_IAdminDisp.java:2229) E at IceInternal.Incoming.invoke(Incoming.java:221) E at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) E at Ice.ConnectionI.dispatch(ConnectionI.java:1145) E at Ice.ConnectionI.message(ConnectionI.java:1056) E at IceInternal.ThreadPool.run(ThreadPool.java:395) E at IceInternal.ThreadPool.access$300(ThreadPool.java:12) E at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) E at java.base/java.lang.Thread.run(Thread.java:829) E E serverExceptionClass = ome.conditions.SecurityViolation E message = Old password is invalid E } ../../../../.venv3/lib64/python3.11/site-packages/omero_api_IAdmin_ice.py:2460: SecurityViolation ______________________________ TestAdmin.test9193 ______________________________ self = @pytest.mark.broken(reason="Is this test still valid?", ticket="11465") def test9193(self): # Test the removal of removing users # from a group when the group in question # may be their last (i.e. default) group g = self.new_group() u = self.new_user(group=g) # Test removing the default group > self.remove_experimenters(g, [u]) test/integration/test_admin.py:240: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/testlib/__init__.py:247: in remove_experimenters admin.removeGroups(user, [group]) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = 89081bd9-fa39-41df-b9c9-68802bf2ec5f/9934711c-ee0a-4a87-98aa-76df37007abfomero.api.IAdmin -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 user = object #0 (::omero::model::Experimenter) { _id = object #1 (::omero::RLong) { _val = 4717 } _d...annotationLinksSeq = { } _annotationLinksLoaded = False _annotationLinksCountPerOwner = { } } groups = [object #0 (::omero::model::ExperimenterGroup) { _id = object #1 (::omero::RLong) { _val = 3670 } ...{ } _annotationLinksLoaded = False _annotationLinksCountPerOwner = { } _description = }] _ctx = None def removeGroups(self, user, groups, _ctx=None): > return _M_omero.api.IAdmin._op_removeGroups.invoke(self, ((user, groups), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E omero.ValidationException: exception ::omero::ValidationException E { E serverStackTrace = ome.conditions.ValidationException: experimenter cannot be a member of only the 'user' group, a different default group is also required E at ome.logic.AdminImpl.removeGroups(AdminImpl.java:813) E at jdk.internal.reflect.GeneratedMethodAccessor599.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.EventHandler.invoke(EventHandler.java:154) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) E at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) E at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy91.removeGroups(Unknown Source) E at jdk.internal.reflect.GeneratedMethodAccessor599.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy91.removeGroups(Unknown Source) E at jdk.internal.reflect.GeneratedMethodAccessor3194.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) E at ome.services.throttling.Callback.run(Callback.java:56) E at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) E at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) E at ome.services.blitz.impl.AdminI.removeGroups_async(AdminI.java:318) E at jdk.internal.reflect.GeneratedMethodAccessor3193.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at omero.cmd.CallContext.invoke(CallContext.java:85) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy92.removeGroups_async(Unknown Source) E at omero.api._IAdminTie.removeGroups_async(_IAdminTie.java:312) E at omero.api._IAdminDisp.___removeGroups(_IAdminDisp.java:1621) E at omero.api._IAdminDisp.__dispatch(_IAdminDisp.java:2377) E at IceInternal.Incoming.invoke(Incoming.java:221) E at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) E at Ice.ConnectionI.dispatch(ConnectionI.java:1145) E at Ice.ConnectionI.message(ConnectionI.java:1056) E at IceInternal.ThreadPool.run(ThreadPool.java:395) E at IceInternal.ThreadPool.access$300(ThreadPool.java:12) E at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) E at java.base/java.lang.Thread.run(Thread.java:829) E E serverExceptionClass = ome.conditions.ValidationException E message = experimenter cannot be a member of only the 'user' group, a different default group is also required E } ../../../../.venv3/lib64/python3.11/site-packages/omero_api_IAdmin_ice.py:2011: ValidationException _________________ TestFiles.testUploadDifferentSizeTicket2337 __________________ self = @pytest.mark.broken(ticket="11610") def testUploadDifferentSizeTicket2337(self): uploaded = tmpfile() ofile = self.client.upload(str(uploaded), type="text/plain") uploaded.write_lines(["abc", "def"]) # Shorten > ofile = self.client.upload( str(uploaded), type="text/plain", ofile=ofile) test/integration/test_files.py:62: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ../../../../.venv3/lib64/python3.11/site-packages/omero/clients.py:878: in upload ofile = up.saveAndReturnObject(ofile) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = 8bc0b114-56d1-4c39-8413-981ea86e1595/630b3e5d-5e21-46a1-81a9-9cb6c88e84abomero.api.IUpdate -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 obj = object #0 (::omero::model::OriginalFile) { _id = object #1 (::omero::RLong) { _val = 6303 } _d...ksCountPerOwner = { } _name = object #60 (::omero::RString) { _val = omerohz4t6zfe.tmp } } _ctx = None def saveAndReturnObject(self, obj, _ctx=None): > return _M_omero.api.IUpdate._op_saveAndReturnObject.invoke(self, ((obj, ), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E omero.OptimisticLockException: exception ::omero::OptimisticLockException E { E serverStackTrace = ome.conditions.OptimisticLockException: You are not authorized to change the update event for ome.model.core.OriginalFile:Id_6303 from ome.model.meta.Event:Id_123648 to ome.model.meta.Event:Id_123647 E You may need to reload the object before continuing. E at ome.security.basic.OmeroInterceptor.managedEvent(OmeroInterceptor.java:1201) E at ome.security.basic.OmeroInterceptor.checkManagedDetails(OmeroInterceptor.java:963) E at ome.security.basic.OmeroInterceptor.resetDetails(OmeroInterceptor.java:465) E at ome.security.basic.OmeroInterceptor.onFlushDirty(OmeroInterceptor.java:239) E at org.hibernate.event.def.DefaultFlushEntityEventListener.invokeInterceptor(DefaultFlushEntityEventListener.java:372) E at org.hibernate.event.def.DefaultFlushEntityEventListener.handleInterception(DefaultFlushEntityEventListener.java:349) E at org.hibernate.event.def.DefaultFlushEntityEventListener.scheduleUpdate(DefaultFlushEntityEventListener.java:287) E at org.hibernate.event.def.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:155) E at org.hibernate.event.def.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:219) E at org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:99) E at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50) E at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216) E at ome.logic.UpdateImpl.afterUpdate(UpdateImpl.java:342) E at ome.logic.UpdateImpl.doAction(UpdateImpl.java:358) E at ome.logic.UpdateImpl.doAction(UpdateImpl.java:349) E at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:135) E at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.EventHandler.invoke(EventHandler.java:154) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) E at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) E at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) E at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) E at jdk.internal.reflect.GeneratedMethodAccessor1126.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) E at ome.services.throttling.Callback.run(Callback.java:56) E at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) E at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) E at ome.services.blitz.impl.UpdateI.saveAndReturnObject_async(UpdateI.java:62) E at jdk.internal.reflect.GeneratedMethodAccessor1125.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at omero.cmd.CallContext.invoke(CallContext.java:85) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy95.saveAndReturnObject_async(Unknown Source) E at omero.api._IUpdateTie.saveAndReturnObject_async(_IUpdateTie.java:92) E at omero.api._IUpdateDisp.___saveAndReturnObject(_IUpdateDisp.java:229) E at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:423) E at IceInternal.Incoming.invoke(Incoming.java:221) E at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) E at Ice.ConnectionI.dispatch(ConnectionI.java:1145) E at Ice.ConnectionI.message(ConnectionI.java:1056) E at IceInternal.ThreadPool.run(ThreadPool.java:395) E at IceInternal.ThreadPool.access$300(ThreadPool.java:12) E at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) E at java.base/java.lang.Thread.run(Thread.java:829) E E serverExceptionClass = ome.conditions.OptimisticLockException E message = You are not authorized to change the update event for ome.model.core.OriginalFile:Id_6303 from ome.model.meta.Event:Id_123648 to ome.model.meta.Event:Id_123647 E You may need to reload the object before continuing. E backOff = 0 E } ../../../../.venv3/lib64/python3.11/site-packages/omero_api_IUpdate_ice.py:163: OptimisticLockException _____________________________ TestIShare.test1172 ______________________________ self = @pytest.mark.broken(reason="shares are image-centric for now") def test1172(self): uuid = self.root.sf.getAdminService().getEventContext().sessionUuid share = self.root.sf.getShareService() query = self.root.sf.getQueryService() # create user client_share1, user1 = self.new_client_and_user() # create dataset with image ds = self.make_dataset(name="dataset-%s" % uuid, client=self.root) img = self.new_image(name='test-img in dataset-%s' % uuid) self.link(ds, img, client=self.root) items = list() p = omero.sys.Parameters() p.map = {"oid": ds.id} sql = ( "select ds from Dataset ds " "join fetch ds.details.owner " "join fetch ds.details.group " "left outer join fetch ds.imageLinks dil " "left outer join fetch dil.child i " "where ds.id=:oid") items.extend(query.findAllByQuery(sql, p)) assert 1 == len(items) # members p.map["eid"] = rlong(user1.id.val) sql = ("select e from Experimenter e " "where e.id =:eid order by e.omeName") ms = query.findAllByQuery(sql, p) sid = share.createShare(("test-share-%s" % uuid), rtime(int(time.time() * 1000 + 86400)), items, ms, [], True) # USER RETRIEVAL # login as user1 share1 = client_share1.sf.getShareService() query1 = client_share1.sf.getQueryService() content = share1.getContents(sid) # Content now contains just the dataset with nothing loaded assert 1 == len(content) # get shared dataset and image when share is activated share1.activate(sid) # retrieve dataset p = omero.sys.Parameters() p.map = {"ids": rlist([ds.id])} sql = ( "select ds from Dataset ds " "join fetch ds.details.owner " "join fetch ds.details.group " "left outer join fetch ds.imageLinks dil " "left outer join fetch dil.child i " "where ds.id in (:ids) order by ds.name") try: res1 = query1.findAllByQuery(sql, p) assert False, "This should throw an exception" except Exception: pass # Now we add all the other elements to the share to prevent # the security violation # # Not working imgs = cntar.getImages("Dataset",[ds.id.val], None) img = query.findByQuery( "select i from Image i join fetch i.datasetLinks dil " "join dil.parent d where d.id = %s " % ds.id.val, None) assert img share.addObject(sid, img) share.addObjects(sid, img.copyDatasetLinks()) assert 3 == len(share.getContents(sid)) # And try again to load them share1.activate(sid) res1 = query1.findAllByQuery(sql, p) > assert len(res1) == 1 E assert 0 == 1 E + where 0 = len([]) test/integration/test_ishare.py:381: AssertionError ____________________________ TestITimeline.test1225 ____________________________ self = @pytest.mark.broken(ticket="1225") def test1225(self): uuid = self.root.sf.getAdminService().getEventContext().sessionUuid update = self.root.sf.getUpdateService() timeline = self.root.sf.getTimelineService() query = self.root.sf.getQueryService() # create dataset to_save = list() for i in range(0, 10): to_save.append(self.new_dataset(name="ds-%i-%s" % (i, uuid))) dss = update.saveAndReturnArray(to_save) # create tag for i in range(0, 10): ds1 = query.get("Dataset", dss[i].id.val) ann = omero.model.TagAnnotationI() ann.textValue = rstring('tag-%i-%s' % (i, uuid)) ann.setDescription(rstring('desc-%i-%s' % (i, uuid))) t_ann = omero.model.DatasetAnnotationLinkI() t_ann.setParent(ds1) t_ann.setChild(ann) update.saveObject(t_ann) p = omero.sys.Parameters() p.map = {} f = omero.sys.Filter() f.ownerId = rlong(0) f.limit = rint(10) p.theFilter = f M = timeline.getMostRecentAnnotationLinks tagids = set([e.child.id.val for e in M(None, ['TagAnnotation'], None, p)]) assert len(tagids) == 10 # And under #9609 tagids = set([e.child.id.val for e in M(None, ['TagAnnotation'], None, p, {"omero.group": "-1"})]) > assert len(tagids) == 10 E assert 6 == 10 E + where 6 = len({1903, 1939, 1990, 9478, 13100, 41436}) test/integration/test_itimeline.py:244: AssertionError ___________________________ TestPermissions.test3136 ___________________________ self = @pytest.mark.broken(ticket="11494") def test3136(self): """ Calls to updateGroup were taking too long because the default value of permissions returned by the server was triggering a full changePermissions event. """ admin = self.root.sf.getAdminService() group = self.new_group(perms="rw----") # Change the name but not the permissions group.name = rstring(self.uuid()) elapsed1, rv = self.timeit(admin.updateGroup, group) # Now change the name and the permissions group.name = rstring(self.uuid()) group.details.permissions = omero.model.PermissionsI("rwr---") elapsed2, rv = self.timeit(admin.updateGroup, group) # Locally this test always fails as the two times are # the same order of magnitude. This may be an indication that # the relevant ticket: # https://trac.openmicroscopy.org/ome/ticket/3136 # is still valid. Does the ticket need re-opening # or does the test condition need relaxing? > assert elapsed1 < (0.1 * elapsed2), \ "elapsed1=%s, elapsed2=%s" % (elapsed1, elapsed2) E AssertionError: elapsed1=0.014118432998657227, elapsed2=0.014019012451171875 E assert 0.014118432998657227 < (0.1 * 0.014019012451171875) test/integration/test_permissions.py:488: AssertionError __________________ TestPermissions.testSaveWithNegOneExplicit __________________ self = @pytest.mark.broken(ticket="11374") def testSaveWithNegOneExplicit(self): # Get a user and services client, user = self.new_client_and_user() # Create a new object with an explicit group admin = client.sf.getAdminService() ec = admin.getEventContext() grp = omero.model.ExperimenterGroupI(ec.groupId, False) tag = omero.model.TagAnnotationI() tag.details.group = grp # Now try to save it in the -1 context update = client.sf.getUpdateService() all_context = {"omero.group": "-1"} > update.saveAndReturnObject(tag, all_context) test/integration/test_permissions.py:586: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = 4a5b3ba0-f097-4128-bc30-cbd8b40f7c76/fd50e89a-cfa3-477d-a296-01654320c53comero.api.IUpdate -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 obj = object #0 (::omero::model::TagAnnotation) { _id = _details = object #1 (::omero::model::Details) { ...nksSeq = { } _annotationLinksLoaded = True _annotationLinksCountPerOwner = {} _textValue = } _ctx = {'omero.group': '-1'} def saveAndReturnObject(self, obj, _ctx=None): > return _M_omero.api.IUpdate._op_saveAndReturnObject.invoke(self, ((obj, ), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E omero.ApiUsageException: exception ::omero::ApiUsageException E { E serverStackTrace = ome.conditions.ApiUsageException: No valid permissions available! DUMMY permissions are not intended for copying. Make sure that you have not passed omero.group=-1 for a save without context E at ome.model.internal.Permissions.(Permissions.java:164) E at ome.security.basic.CurrentDetails.createDetails(CurrentDetails.java:439) E at ome.security.basic.OmeroInterceptor.newTransientDetails(OmeroInterceptor.java:700) E at ome.security.basic.OmeroInterceptor.onSave(OmeroInterceptor.java:187) E at org.hibernate.event.def.AbstractSaveEventListener.substituteValuesIfNecessary(AbstractSaveEventListener.java:413) E at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:292) E at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:203) E at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:143) E at org.hibernate.event.def.DefaultMergeEventListener.saveTransientEntity(DefaultMergeEventListener.java:415) E at org.hibernate.event.def.DefaultMergeEventListener.mergeTransientEntity(DefaultMergeEventListener.java:341) E at org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:303) E at org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener.entityIsTransient(IdTransferringMergeEventListener.java:62) E at ome.security.basic.MergeEventListener.entityIsTransient(MergeEventListener.java:154) E at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:258) E at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:87) E at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:84) E at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:73) E at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:867) E at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:851) E at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:855) E at ome.logic.UpdateImpl.internalMerge(UpdateImpl.java:313) E at ome.logic.UpdateImpl$2.run(UpdateImpl.java:138) E at ome.logic.UpdateImpl$2.run(UpdateImpl.java:135) E at ome.logic.UpdateImpl.doAction(UpdateImpl.java:357) E at ome.logic.UpdateImpl.doAction(UpdateImpl.java:349) E at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:135) E at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.EventHandler.invoke(EventHandler.java:154) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) E at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) E at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) E at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) E at jdk.internal.reflect.GeneratedMethodAccessor1126.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) E at ome.services.throttling.Callback.run(Callback.java:56) E at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) E at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) E at ome.services.blitz.impl.UpdateI.saveAndReturnObject_async(UpdateI.java:62) E at jdk.internal.reflect.GeneratedMethodAccessor1125.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at omero.cmd.CallContext.invoke(CallContext.java:85) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy95.saveAndReturnObject_async(Unknown Source) E at omero.api._IUpdateTie.saveAndReturnObject_async(_IUpdateTie.java:92) E at omero.api._IUpdateDisp.___saveAndReturnObject(_IUpdateDisp.java:229) E at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:423) E at IceInternal.Incoming.invoke(Incoming.java:221) E at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) E at Ice.ConnectionI.dispatch(ConnectionI.java:1145) E at Ice.ConnectionI.message(ConnectionI.java:1056) E at IceInternal.ThreadPool.run(ThreadPool.java:395) E at IceInternal.ThreadPool.access$300(ThreadPool.java:12) E at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) E at java.base/java.lang.Thread.run(Thread.java:829) E E serverExceptionClass = ome.conditions.ApiUsageException E message = No valid permissions available! DUMMY permissions are not intended for copying. Make sure that you have not passed omero.group=-1 for a save without context E } ../../../../.venv3/lib64/python3.11/site-packages/omero_api_IUpdate_ice.py:163: ApiUsageException ____________________ TestPermissions.testSaveWithNegBadLink ____________________ self = @pytest.mark.broken(ticket="11374") def testSaveWithNegBadLink(self): # ticket:8194 # Get a user and services client, user = self.new_client_and_user() admin = client.sf.getAdminService() group1 = admin.getGroup(admin.getEventContext().groupId) group2 = self.new_group(experimenters=[user]) for x in (group1, group2): x.unload() admin.getEventContext() # Refresh # Create a new object with a bad link image = self.new_image() image.details.group = group1 tag = omero.model.TagAnnotationI() tag.details.group = group2 link = image.linkAnnotation(tag) link.details.group = group2 # Now try to save it in the -1 context update = client.sf.getUpdateService() all_context = {"omero.group": "-1"} # Bad links should be detected and # a security violation raised. with pytest.raises(omero.GroupSecurityViolation): > update.saveAndReturnObject(image, all_context) test/integration/test_permissions.py:635: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = 01c148fa-54b9-4ab1-a085-ca990efe82d0/8066a30d-8612-4656-b32d-3459b605cb3eomero.api.IUpdate -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 obj = object #0 (::omero::model::Image) { _id = _details = object #1 (::omero::model::Details) { _...225d36-b109-4c77-bc12-187daa3ec673 } _description = object #14 (::omero::RString) { _val = } } _ctx = {'omero.group': '-1'} def saveAndReturnObject(self, obj, _ctx=None): > return _M_omero.api.IUpdate._op_saveAndReturnObject.invoke(self, ((obj, ), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E omero.ApiUsageException: exception ::omero::ApiUsageException E { E serverStackTrace = ome.conditions.ApiUsageException: No valid permissions available! DUMMY permissions are not intended for copying. Make sure that you have not passed omero.group=-1 for a save without context E at ome.model.internal.Permissions.(Permissions.java:164) E at ome.security.basic.CurrentDetails.createDetails(CurrentDetails.java:439) E at ome.security.basic.OmeroInterceptor.newTransientDetails(OmeroInterceptor.java:700) E at ome.security.basic.OmeroInterceptor.onSave(OmeroInterceptor.java:187) E at org.hibernate.event.def.AbstractSaveEventListener.substituteValuesIfNecessary(AbstractSaveEventListener.java:413) E at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:292) E at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:203) E at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:143) E at org.hibernate.event.def.DefaultMergeEventListener.saveTransientEntity(DefaultMergeEventListener.java:415) E at org.hibernate.event.def.DefaultMergeEventListener.mergeTransientEntity(DefaultMergeEventListener.java:341) E at org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:303) E at org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener.entityIsTransient(IdTransferringMergeEventListener.java:62) E at ome.security.basic.MergeEventListener.entityIsTransient(MergeEventListener.java:154) E at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:258) E at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:87) E at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:84) E at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:73) E at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:867) E at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:851) E at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:855) E at ome.logic.UpdateImpl.internalMerge(UpdateImpl.java:313) E at ome.logic.UpdateImpl$2.run(UpdateImpl.java:138) E at ome.logic.UpdateImpl$2.run(UpdateImpl.java:135) E at ome.logic.UpdateImpl.doAction(UpdateImpl.java:357) E at ome.logic.UpdateImpl.doAction(UpdateImpl.java:349) E at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:135) E at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.EventHandler.invoke(EventHandler.java:154) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) E at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) E at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) E at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) E at jdk.internal.reflect.GeneratedMethodAccessor1126.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) E at ome.services.throttling.Callback.run(Callback.java:56) E at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) E at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) E at ome.services.blitz.impl.UpdateI.saveAndReturnObject_async(UpdateI.java:62) E at jdk.internal.reflect.GeneratedMethodAccessor1125.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at omero.cmd.CallContext.invoke(CallContext.java:85) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy95.saveAndReturnObject_async(Unknown Source) E at omero.api._IUpdateTie.saveAndReturnObject_async(_IUpdateTie.java:92) E at omero.api._IUpdateDisp.___saveAndReturnObject(_IUpdateDisp.java:229) E at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:423) E at IceInternal.Incoming.invoke(Incoming.java:221) E at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) E at Ice.ConnectionI.dispatch(ConnectionI.java:1145) E at Ice.ConnectionI.message(ConnectionI.java:1056) E at IceInternal.ThreadPool.run(ThreadPool.java:395) E at IceInternal.ThreadPool.access$300(ThreadPool.java:12) E at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) E at java.base/java.lang.Thread.run(Thread.java:829) E E serverExceptionClass = ome.conditions.ApiUsageException E message = No valid permissions available! DUMMY permissions are not intended for copying. Make sure that you have not passed omero.group=-1 for a save without context E } ../../../../.venv3/lib64/python3.11/site-packages/omero_api_IUpdate_ice.py:163: ApiUsageException _______________________ TestPermissions.testSaveBadLink ________________________ self = @pytest.mark.broken(ticket="11375") def testSaveBadLink(self): # Get a user and services client, user = self.new_client_and_user() admin = client.sf.getAdminService() group1 = admin.getGroup(admin.getEventContext().groupId) group2 = self.new_group(experimenters=[user]) for x in (group1, group2): x.unload() admin.getEventContext() # Refresh # Create a new object with a bad link image = self.new_image() image.details.group = group1 tag = omero.model.TagAnnotationI() tag.details.group = group2 link = image.linkAnnotation(tag) link.details.group = group2 # Now try to save it update = client.sf.getUpdateService() # Bad links should be detected and # a security violation raised. with pytest.raises(omero.GroupSecurityViolation): > update.saveAndReturnObject(image) test/integration/test_permissions.py:664: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = 15aa8c0a-3070-4a55-97ec-a7261f8481a3/03786a78-6f5e-463b-97dd-6d3a64404ee6omero.api.IUpdate -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 obj = object #0 (::omero::model::Image) { _id = _details = object #1 (::omero::model::Details) { _...2e448f-a751-44f3-8fd5-f327036ef8ce } _description = object #14 (::omero::RString) { _val = } } _ctx = None def saveAndReturnObject(self, obj, _ctx=None): > return _M_omero.api.IUpdate._op_saveAndReturnObject.invoke(self, ((obj, ), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E omero.SecurityViolation: exception ::omero::SecurityViolation E { E serverStackTrace = ome.conditions.SecurityViolation: You are not authorized to set the ExperimenterGroup for ome.model.annotations.TagAnnotation:Id_41591 to ome.model.meta.ExperimenterGroup:Id_3681 E at ome.security.basic.OmeroInterceptor.newTransientDetails(OmeroInterceptor.java:785) E at ome.security.basic.OmeroInterceptor.onSave(OmeroInterceptor.java:187) E at org.hibernate.event.def.AbstractSaveEventListener.substituteValuesIfNecessary(AbstractSaveEventListener.java:413) E at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:292) E at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:203) E at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:143) E at org.hibernate.event.def.DefaultMergeEventListener.saveTransientEntity(DefaultMergeEventListener.java:415) E at org.hibernate.event.def.DefaultMergeEventListener.mergeTransientEntity(DefaultMergeEventListener.java:341) E at org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:303) E at org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener.entityIsTransient(IdTransferringMergeEventListener.java:62) E at ome.security.basic.MergeEventListener.entityIsTransient(MergeEventListener.java:154) E at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:258) E at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:87) E at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:877) E at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:859) E at org.hibernate.engine.CascadingAction$6.cascade(CascadingAction.java:279) E at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:392) E at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:335) E at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204) E at org.hibernate.engine.Cascade.cascade(Cascade.java:161) E at org.hibernate.event.def.AbstractSaveEventListener.cascadeBeforeSave(AbstractSaveEventListener.java:450) E at org.hibernate.event.def.DefaultMergeEventListener.mergeTransientEntity(DefaultMergeEventListener.java:336) E at org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:303) E at org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener.entityIsTransient(IdTransferringMergeEventListener.java:62) E at ome.security.basic.MergeEventListener.entityIsTransient(MergeEventListener.java:154) E at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:258) E at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:87) E at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:877) E at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:859) E at org.hibernate.engine.CascadingAction$6.cascade(CascadingAction.java:279) E at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:392) E at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:335) E at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204) E at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:425) E at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:362) E at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:338) E at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204) E at org.hibernate.engine.Cascade.cascade(Cascade.java:161) E at org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:475) E at org.hibernate.event.def.DefaultMergeEventListener.mergeTransientEntity(DefaultMergeEventListener.java:388) E at org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:303) E at org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener.entityIsTransient(IdTransferringMergeEventListener.java:62) E at ome.security.basic.MergeEventListener.entityIsTransient(MergeEventListener.java:154) E at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:258) E at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:87) E at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:84) E at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:73) E at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:867) E at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:851) E at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:855) E at ome.logic.UpdateImpl.internalMerge(UpdateImpl.java:313) E at ome.logic.UpdateImpl$2.run(UpdateImpl.java:138) E at ome.logic.UpdateImpl$2.run(UpdateImpl.java:135) E at ome.logic.UpdateImpl.doAction(UpdateImpl.java:357) E at ome.logic.UpdateImpl.doAction(UpdateImpl.java:349) E at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:135) E at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.EventHandler.invoke(EventHandler.java:154) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) E at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) E at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) E at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) E at jdk.internal.reflect.GeneratedMethodAccessor1126.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) E at ome.services.throttling.Callback.run(Callback.java:56) E at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) E at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) E at ome.services.blitz.impl.UpdateI.saveAndReturnObject_async(UpdateI.java:62) E at jdk.internal.reflect.GeneratedMethodAccessor1125.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at omero.cmd.CallContext.invoke(CallContext.java:85) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy95.saveAndReturnObject_async(Unknown Source) E at omero.api._IUpdateTie.saveAndReturnObject_async(_IUpdateTie.java:92) E at omero.api._IUpdateDisp.___saveAndReturnObject(_IUpdateDisp.java:229) E at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:423) E at IceInternal.Incoming.invoke(Incoming.java:221) E at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) E at Ice.ConnectionI.dispatch(ConnectionI.java:1145) E at Ice.ConnectionI.message(ConnectionI.java:1056) E at IceInternal.ThreadPool.run(ThreadPool.java:395) E at IceInternal.ThreadPool.access$300(ThreadPool.java:12) E at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) E at java.base/java.lang.Thread.run(Thread.java:829) E E serverExceptionClass = ome.conditions.SecurityViolation E message = You are not authorized to set the ExperimenterGroup for ome.model.annotations.TagAnnotation:Id_41591 to ome.model.meta.ExperimenterGroup:Id_3681 E } ../../../../.venv3/lib64/python3.11/site-packages/omero_api_IUpdate_ice.py:163: SecurityViolation ______ TestPermissions.testUseOfRawFileBeanScriptReadCorrectGroupAndUser _______ self = @pytest.mark.broken(ticket="11539") def testUseOfRawFileBeanScriptReadCorrectGroupAndUser(self): > self.assertValidScript(lambda v: { 'omero.group': str(v.details.group.id.val), 'omero.user': str(v.details.owner.id.val) }) test/integration/test_permissions.py:831: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/test_permissions.py:813: in assertValidScript store.setFileId(script.id.val, ctx) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = e39daad9-30e2-44cf-af58-f052ca8d60f7/0e05ed12-866c-48f8-ade1-fd9accb706d4omero.api.RawFileStore -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 fileId = 1 _ctx = {'omero.client.uuid': '404f3f66-dada-4730-8a09-1bc1d3fc610c', 'omero.group': '1', 'omero.session.uuid': 'e39daad9-30e2-44cf-af58-f052ca8d60f7', 'omero.user': '0'} def setFileId(self, fileId, _ctx=None): > return _M_omero.api.RawFileStore._op_setFileId.invoke(self, ((fileId, ), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E Ice.UnknownException: exception ::Ice::UnknownException E { E unknown = ome.conditions.SecurityViolation: User 4726 is not an admin and so cannot set uid to 0 E at ome.security.basic.BasicEventContext.checkAndInitialize(BasicEventContext.java:141) E at ome.security.basic.CurrentDetails.checkAndInitialize(CurrentDetails.java:317) E at ome.security.basic.BasicSecuritySystem.loadEventContext(BasicSecuritySystem.java:449) E at ome.security.basic.EventHandler.doLogin(EventHandler.java:210) E at ome.security.basic.EventHandler.invoke(EventHandler.java:146) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) E at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) E at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy74.doWork(Unknown Source) E at ome.services.util.Executor$Impl.execute(Executor.java:447) E at ome.services.blitz.repo.RepositoryDaoImpl.getFile(RepositoryDaoImpl.java:866) E at ome.services.blitz.repo.PublicRepositoryI.checkId(PublicRepositoryI.java:823) E at ome.services.blitz.repo.PublicRepositoryI.fileById(PublicRepositoryI.java:367) E at omero.grid._RepositoryTie.fileById(_RepositoryTie.java:78) E at omero.grid._RepositoryDisp.___fileById(_RepositoryDisp.java:393) E at omero.grid._RepositoryDisp.__dispatch(_RepositoryDisp.java:538) E at IceInternal.Incoming.invoke(Incoming.java:221) E at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) E at Ice.ConnectionI.dispatch(ConnectionI.java:1145) E at Ice.ConnectionI.message(ConnectionI.java:1056) E at IceInternal.ThreadPool.run(ThreadPool.java:395) E at IceInternal.ThreadPool.access$300(ThreadPool.java:12) E at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) E at java.base/java.lang.Thread.run(Thread.java:829) E E } ../../../../.venv3/lib64/python3.11/site-packages/omero_api_RawFileStore_ice.py:200: UnknownException _________________________ TestRFS.testTicket1961Basic __________________________ self = @pytest.mark.broken(ticket="11534") def testTicket1961Basic(self): ofile = self.file() rfs = self.client.sf.createRawFileStore() rfs.setFileId(ofile.id.val) rfs.write([0, 1, 2, 3], 0, 4) rfs.close() > self.check_file(ofile) test/integration/test_rawfilestore.py:49: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = ofile = object #0 (::omero::model::OriginalFile) { _id = object #1 (::omero::RLong) { _val = 6304 } _d...annotationLinksCountPerOwner = { } _name = object #26 (::omero::RString) { _val = test } } client = def check_file(self, ofile, client=None): if client is None: client = self.client query = client.sf.getQueryService() ofile = query.get("OriginalFile", ofile.id.val) assert ofile.size.val != -1 > assert ofile.hash.val != "" E AssertionError: assert '' != '' E + where '' = object #0 (::omero::RString)\n{\n _val = \n}.val E + where object #0 (::omero::RString)\n{\n _val = \n} = object #0 (::omero::model::OriginalFile)\n{\n _id = object #1 (::omero::RLong)\n {\n _val = 6304\n }\n _details = object #2 (::omero::model::Details)\n {\n _owner = object #3 (::omero::model::Experimenter)\n {\n _id = object #4 (::omero::RLong)\n {\n _val = 4727\n }\n _details = \n _loaded = False\n _version = \n _groupExperimenterMapSeq = \n {\n }\n _groupExperimenterMapLoaded = False\n _omeName = \n _firstName = \n _middleName = \n _lastName = \n _institution = \n _ldap = \n _email = \n _config = \n {\n }\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n }\n _group = object #5 (::omero::model::ExperimenterGroup)\n {\n _id = object #6 (::omero::RLong)\n {\n _val = 3683\n }\n _details = object #7 (::... }\n groupPermissions = object #20 (::omero::model::Permissions)\n {\n _restrictions = \n {\n }\n _extendedRestrictions = \n {\n }\n _perm1 = -120\n }\n }\n }\n _loaded = True\n _version = \n _pixelsFileMapsSeq = \n {\n }\n _pixelsFileMapsLoaded = False\n _pixelsFileMapsCountPerOwner = \n {\n }\n _path = object #21 (::omero::RString)\n {\n _val = /tmp/test\n }\n _repo = \n _size = object #22 (::omero::RLong)\n {\n _val = 4\n }\n _atime = \n _mtime = object #23 (::omero::RTime)\n {\n _val = 1765251698327\n }\n _ctime = \n _hasher = \n _hash = object #24 (::omero::RString)\n {\n _val = \n }\n _mimetype = object #25 (::omero::RString)\n {\n _val = application/octet-stream\n }\n _filesetEntriesSeq = \n {\n }\n _filesetEntriesLoaded = True\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n _name = object #26 (::omero::RString)\n {\n _val = test\n }\n}.hash test/integration/test_rawfilestore.py:40: AssertionError ____________________ TestRFS.testTicket1961WithKillSession _____________________ self = @pytest.mark.broken(ticket="11534") def testTicket1961WithKillSession(self): ofile = self.file() grp = self.ctx.groupName session = self.client.sf.getSessionService().createUserSession( 1 * 1000, 10000, grp) properties = self.client.getPropertyMap() c = omero.client(properties) s = c.joinSession(session.uuid.val) rfs = s.createRawFileStore() rfs.setFileId(ofile.id.val) rfs.write([0, 1, 2, 3], 0, 4) c.killSession() > self.check_file(ofile) test/integration/test_rawfilestore.py:67: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = ofile = object #0 (::omero::model::OriginalFile) { _id = object #1 (::omero::RLong) { _val = 6305 } _d...annotationLinksCountPerOwner = { } _name = object #26 (::omero::RString) { _val = test } } client = def check_file(self, ofile, client=None): if client is None: client = self.client query = client.sf.getQueryService() ofile = query.get("OriginalFile", ofile.id.val) assert ofile.size.val != -1 > assert ofile.hash.val != "" E AssertionError: assert '' != '' E + where '' = object #0 (::omero::RString)\n{\n _val = \n}.val E + where object #0 (::omero::RString)\n{\n _val = \n} = object #0 (::omero::model::OriginalFile)\n{\n _id = object #1 (::omero::RLong)\n {\n _val = 6305\n }\n _details = object #2 (::omero::model::Details)\n {\n _owner = object #3 (::omero::model::Experimenter)\n {\n _id = object #4 (::omero::RLong)\n {\n _val = 4727\n }\n _details = \n _loaded = False\n _version = \n _groupExperimenterMapSeq = \n {\n }\n _groupExperimenterMapLoaded = False\n _omeName = \n _firstName = \n _middleName = \n _lastName = \n _institution = \n _ldap = \n _email = \n _config = \n {\n }\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n }\n _group = object #5 (::omero::model::ExperimenterGroup)\n {\n _id = object #6 (::omero::RLong)\n {\n _val = 3683\n }\n _details = object #7 (::... }\n groupPermissions = object #20 (::omero::model::Permissions)\n {\n _restrictions = \n {\n }\n _extendedRestrictions = \n {\n }\n _perm1 = -120\n }\n }\n }\n _loaded = True\n _version = \n _pixelsFileMapsSeq = \n {\n }\n _pixelsFileMapsLoaded = False\n _pixelsFileMapsCountPerOwner = \n {\n }\n _path = object #21 (::omero::RString)\n {\n _val = /tmp/test\n }\n _repo = \n _size = object #22 (::omero::RLong)\n {\n _val = 4\n }\n _atime = \n _mtime = object #23 (::omero::RTime)\n {\n _val = 1765251698388\n }\n _ctime = \n _hasher = \n _hash = object #24 (::omero::RString)\n {\n _val = \n }\n _mimetype = object #25 (::omero::RString)\n {\n _val = application/octet-stream\n }\n _filesetEntriesSeq = \n {\n }\n _filesetEntriesLoaded = True\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n _name = object #26 (::omero::RString)\n {\n _val = test\n }\n}.hash test/integration/test_rawfilestore.py:40: AssertionError __________________________ TestRFS.testTicket2161Save __________________________ self = @pytest.mark.broken(ticket="11534") def testTicket2161Save(self): ofile = self.file() rfs = self.client.sf.createRawFileStore() rfs.setFileId(ofile.id.val) rfs.write([0, 1, 2, 3], 0, 4) ofile = rfs.save() > self.check_file(ofile) test/integration/test_rawfilestore.py:76: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = ofile = object #0 (::omero::model::OriginalFile) { _id = object #1 (::omero::RLong) { _val = 6306 } _d...annotationLinksCountPerOwner = { } _name = object #26 (::omero::RString) { _val = test } } client = def check_file(self, ofile, client=None): if client is None: client = self.client query = client.sf.getQueryService() ofile = query.get("OriginalFile", ofile.id.val) assert ofile.size.val != -1 > assert ofile.hash.val != "" E AssertionError: assert '' != '' E + where '' = object #0 (::omero::RString)\n{\n _val = \n}.val E + where object #0 (::omero::RString)\n{\n _val = \n} = object #0 (::omero::model::OriginalFile)\n{\n _id = object #1 (::omero::RLong)\n {\n _val = 6306\n }\n _details = object #2 (::omero::model::Details)\n {\n _owner = object #3 (::omero::model::Experimenter)\n {\n _id = object #4 (::omero::RLong)\n {\n _val = 4727\n }\n _details = \n _loaded = False\n _version = \n _groupExperimenterMapSeq = \n {\n }\n _groupExperimenterMapLoaded = False\n _omeName = \n _firstName = \n _middleName = \n _lastName = \n _institution = \n _ldap = \n _email = \n _config = \n {\n }\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n }\n _group = object #5 (::omero::model::ExperimenterGroup)\n {\n _id = object #6 (::omero::RLong)\n {\n _val = 3683\n }\n _details = object #7 (::... }\n groupPermissions = object #20 (::omero::model::Permissions)\n {\n _restrictions = \n {\n }\n _extendedRestrictions = \n {\n }\n _perm1 = -120\n }\n }\n }\n _loaded = True\n _version = \n _pixelsFileMapsSeq = \n {\n }\n _pixelsFileMapsLoaded = False\n _pixelsFileMapsCountPerOwner = \n {\n }\n _path = object #21 (::omero::RString)\n {\n _val = /tmp/test\n }\n _repo = \n _size = object #22 (::omero::RLong)\n {\n _val = 4\n }\n _atime = \n _mtime = object #23 (::omero::RTime)\n {\n _val = 1765251698423\n }\n _ctime = \n _hasher = \n _hash = object #24 (::omero::RString)\n {\n _val = \n }\n _mimetype = object #25 (::omero::RString)\n {\n _val = application/octet-stream\n }\n _filesetEntriesSeq = \n {\n }\n _filesetEntriesLoaded = True\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n _name = object #26 (::omero::RString)\n {\n _val = test\n }\n}.hash test/integration/test_rawfilestore.py:40: AssertionError _____________________________ TestRFS.testNoWrite ______________________________ self = @pytest.mark.broken(ticket="11534") def testNoWrite(self): group = self.new_group(perms="rwr---") client1 = self.new_client(group=group) client2 = self.new_client(group=group) ofile = self.file(client=client1) rfs = client1.sf.createRawFileStore() rfs.setFileId(ofile.id.val) rfs.write(b"0123", 0, 4) rfs.close() > self.check_file(ofile, client=client1) test/integration/test_rawfilestore.py:94: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = ofile = object #0 (::omero::model::OriginalFile) { _id = object #1 (::omero::RLong) { _val = 6307 } _d...annotationLinksCountPerOwner = { } _name = object #26 (::omero::RString) { _val = test } } client = def check_file(self, ofile, client=None): if client is None: client = self.client query = client.sf.getQueryService() ofile = query.get("OriginalFile", ofile.id.val) assert ofile.size.val != -1 > assert ofile.hash.val != "" E AssertionError: assert '' != '' E + where '' = object #0 (::omero::RString)\n{\n _val = \n}.val E + where object #0 (::omero::RString)\n{\n _val = \n} = object #0 (::omero::model::OriginalFile)\n{\n _id = object #1 (::omero::RLong)\n {\n _val = 6307\n }\n _details = object #2 (::omero::model::Details)\n {\n _owner = object #3 (::omero::model::Experimenter)\n {\n _id = object #4 (::omero::RLong)\n {\n _val = 4728\n }\n _details = \n _loaded = False\n _version = \n _groupExperimenterMapSeq = \n {\n }\n _groupExperimenterMapLoaded = False\n _omeName = \n _firstName = \n _middleName = \n _lastName = \n _institution = \n _ldap = \n _email = \n _config = \n {\n }\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n }\n _group = object #5 (::omero::model::ExperimenterGroup)\n {\n _id = object #6 (::omero::RLong)\n {\n _val = 3684\n }\n _details = object #7 (::... }\n groupPermissions = object #20 (::omero::model::Permissions)\n {\n _restrictions = \n {\n }\n _extendedRestrictions = \n {\n }\n _perm1 = -56\n }\n }\n }\n _loaded = True\n _version = \n _pixelsFileMapsSeq = \n {\n }\n _pixelsFileMapsLoaded = False\n _pixelsFileMapsCountPerOwner = \n {\n }\n _path = object #21 (::omero::RString)\n {\n _val = /tmp/test\n }\n _repo = \n _size = object #22 (::omero::RLong)\n {\n _val = 4\n }\n _atime = \n _mtime = object #23 (::omero::RTime)\n {\n _val = 1765251703366\n }\n _ctime = \n _hasher = \n _hash = object #24 (::omero::RString)\n {\n _val = \n }\n _mimetype = object #25 (::omero::RString)\n {\n _val = application/octet-stream\n }\n _filesetEntriesSeq = \n {\n }\n _filesetEntriesLoaded = True\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n _name = object #26 (::omero::RString)\n {\n _val = test\n }\n}.hash test/integration/test_rawfilestore.py:40: AssertionError __________________ TestRepoRawFileStore.testFailedWriteNoFile __________________ self = @pytest.mark.broken(ticket="11610") def testFailedWriteNoFile(self): # Without a single write, no file is produced rfs = self.repoPrx.file(self.repo_filename, "rw") # create empty file rfs.close() rfs = self.repoPrx.file(self.repo_filename, "r") > with pytest.raises(omero.ResourceError): E Failed: DID NOT RAISE test/integration/test_reporawfilestore.py:67: Failed ______________________ TestScripts.testAutoFillTicket2326 ______________________ self = @pytest.mark.broken(ticket="11539") def testAutoFillTicket2326(self): SCRIPT = """if True: import omero.scripts import omero.rtypes client = omero.scripts.client( "ticket2326", omero.scripts.Long("width", optional=True)) width = client.getInput("width") print(width) client.setOutput( "noWidthKey", omero.rtypes.rbool("width" not in client.getInputKeys())) client.setOutput("widthIsNull", omero.rtypes.rbool(width is None)) """ impl = omero.processor.usermode_processor(self.client) svc = self.client.sf.getScriptService() try: scriptID = svc.uploadScript("/test/testAutoFillTicket2326", SCRIPT) > process = svc.runScript(scriptID, {}, None) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/test_scripts.py:385: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = 23686a99-cde5-4dc2-a17b-d4e97400a896/8c0a348c-883a-4e10-a4b6-8dd7a5537f13omero.api.IScript -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 scriptID = 6312, inputs = {}, waitSecs = None, _ctx = None def runScript(self, scriptID, inputs, waitSecs, _ctx=None): > return _M_omero.api.IScript._op_runScript.invoke(self, ((scriptID, inputs, waitSecs), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E omero.NoProcessorAvailable: exception ::omero::NoProcessorAvailable E { E serverStackTrace = E serverExceptionClass = E message = No processor available! [0 response(s)] E processorCount = 0 E } ../../../../.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py:935: NoProcessorAvailable ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.processor.ProcessorI:processor.py:814 Registering processor JQ%<\"G`TGkwCx&o#0HY!/UsermodeProcessor-00b78708-92bc-469a-bb33-4e516d1a804c -t -e 1.1:tcp -h 127.0.0.1 -p 35631 -t 60000 INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4731, group=3686, script=5118 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4731, group=3686, script=5118 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } INFO omero.remote:decorators.py:75 Rslt: INFO omero.remote:decorators.py:75 Rslt: INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4731, group=3686, script=5119 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } INFO omero.remote:decorators.py:75 Rslt: ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4731, group=3686, script=5119 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } INFO omero.remote:decorators.py:75 Rslt: INFO omero.processor.ProcessorI:__init__.py:597 Cleaning up INFO omero.processor.ProcessorI:__init__.py:599 Done INFO omero.util.Resources:__init__.py:669 Halted ______________ TestScripts.testParamLoadingPerformanceTicket2285 _______________ self = @pytest.mark.broken(reason="Minor performance failure", ticket="11539") def testParamLoadingPerformanceTicket2285(self): root_client = self.new_client(system=True) svc = root_client.sf.getScriptService() SCRIPT = """if True: import omero.model as OM import omero.rtypes as OR import omero.scripts as OS c = OS.client("perf test", OS.Long("a", min=0, max=5), OS.String("b", values=("a","b","c")), OS.List("c").ofType(OM.ImageI)) """ upload_time, scriptID = self.timeit( svc.uploadOfficialScript, "/test/perf%s.py" % self.uuid(), SCRIPT) impl = omero.processor.usermode_processor(root_client) try: params_time, params = self.timeit(svc.getParams, scriptID) > assert params_time < (upload_time / 10), \ "upload_time(%s) <= 10 * params_time(%s)!" % \ (upload_time, params_time) E AssertionError: upload_time(0.09987521171569824) <= 10 * params_time(0.6016995906829834)! E assert 0.6016995906829834 < (0.09987521171569824 / 10) test/integration/test_scripts.py:419: AssertionError ------------------------------ Captured log call ------------------------------- INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4732, group=3687, script=5120 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 858, in willAccept handle.close() File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_ServicesF_ice.py", line 287, in close return _M_omero.api.StatefulServiceInterface._op_close.invoke(self, ((), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.SecurityViolation: exception ::omero::SecurityViolation { serverStackTrace = ome.conditions.SecurityViolation: User 4731 is not a member of group 3687 and cannot login at ome.security.basic.BasicSecuritySystem.loadEventContext(BasicSecuritySystem.java:514) at ome.security.basic.EventHandler.doLogin(EventHandler.java:210) at ome.security.basic.EventHandler.invoke(EventHandler.java:146) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:216) at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:200) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy103.close(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor579.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy103.close(Unknown Source) at ome.services.blitz.impl.AbstractCloseableAmdServant.close_async(AbstractCloseableAmdServant.java:90) at jdk.internal.reflect.GeneratedMethodAccessor607.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy104.close_async(Unknown Source) at omero.api._JobHandleTie.close_async(_JobHandleTie.java:144) at omero.api._StatefulServiceInterfaceDisp.___close(_StatefulServiceInterfaceDisp.java:185) at omero.api._JobHandleDisp.__dispatch(_JobHandleDisp.java:597) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.SecurityViolation message = User 4731 is not a member of group 3687 and cannot login } INFO omero.remote:decorators.py:75 Rslt: INFO omero.remote:decorators.py:75 Rslt: INFO omero.remote:decorators.py:70 Meth: ProcessorI.parseJob INFO omero.processor.ProcessorI:processor.py:912 parseJob: Session = bbe1aa8d-b1b2-4f6b-a1bd-8ea27bce7673, JobId = 5120 INFO omero.processor.ProcessorI:processor.py:1034 Using launcher: /home/omero/workspace/OMERO-test-integration/.venv3/bin/python3.11 INFO omero.processor.ProcessorI:processor.py:1035 Using process: INFO omero.processor.ProcessI:processor.py:137 Created bbe1aa8d-b1b2-4f6b-a1bd-8ea27bce7673 in /home/omero/omero/tmp/omero_omero/2374166/processifmwiguk.dir INFO omero.remote:decorators.py:78 Excp: 'NoneType' object has no attribute 'add' WARNING omero.remote:decorators.py:82 raised a non-ServerError (): 'NoneType' object has no attribute 'add' INFO omero.util.Resources:__init__.py:652 Starting INFO omero.processor.ProcessorI:processor.py:814 Registering processor "A5<}\\4nZKPyN-.50>:\\#/UsermodeProcessor-2525c379-cbf7-48bf-8ccf-6fcf3f21056c" -t -e 1.1:tcp -h 127.0.0.1 -p 35631 -t 60000 INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4732, group=3687, script=5121 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 858, in willAccept handle.close() File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_ServicesF_ice.py", line 287, in close return _M_omero.api.StatefulServiceInterface._op_close.invoke(self, ((), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.SecurityViolation: exception ::omero::SecurityViolation { serverStackTrace = ome.conditions.SecurityViolation: User 4731 is not a member of group 3687 and cannot login at ome.security.basic.BasicSecuritySystem.loadEventContext(BasicSecuritySystem.java:514) at ome.security.basic.EventHandler.doLogin(EventHandler.java:210) at ome.security.basic.EventHandler.invoke(EventHandler.java:146) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:216) at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:200) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy103.close(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor579.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy103.close(Unknown Source) at ome.services.blitz.impl.AbstractCloseableAmdServant.close_async(AbstractCloseableAmdServant.java:90) at jdk.internal.reflect.GeneratedMethodAccessor607.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy104.close_async(Unknown Source) at omero.api._JobHandleTie.close_async(_JobHandleTie.java:144) at omero.api._StatefulServiceInterfaceDisp.___close(_StatefulServiceInterfaceDisp.java:185) at omero.api._JobHandleDisp.__dispatch(_JobHandleDisp.java:597) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.SecurityViolation message = User 4731 is not a member of group 3687 and cannot login } INFO omero.remote:decorators.py:75 Rslt: ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4732, group=3687, script=5121 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } INFO omero.remote:decorators.py:75 Rslt: INFO omero.remote:decorators.py:75 Rslt: INFO omero.processor.ProcessorI:__init__.py:597 Cleaning up INFO omero.processor.ProcessorI:__init__.py:599 Done INFO omero.util.Resources:__init__.py:669 Halted _____________________________ TestScripts.test3527 _____________________________ self = @pytest.mark.broken(ticket="11610") def test3527(self): SCRIPT = """if True: import omero.scripts import omero.rtypes client = omero.scripts.client("ticket3527", \ omero.scripts.Long("gid", out=True)) ec = client.sf.getAdminService().getEventContext() gid = ec.groupId client.setOutput("gid", omero.rtypes.rlong(gid)) """ impl = omero.processor.usermode_processor(self.client) svc = self.client.sf.getScriptService() try: scriptID = svc.uploadScript("/test/test3527", SCRIPT) > process = svc.runScript(scriptID, {}, None) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/integration/test_scripts.py:528: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = 23686a99-cde5-4dc2-a17b-d4e97400a896/8c0a348c-883a-4e10-a4b6-8dd7a5537f13omero.api.IScript -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 scriptID = 6315, inputs = {}, waitSecs = None, _ctx = None def runScript(self, scriptID, inputs, waitSecs, _ctx=None): > return _M_omero.api.IScript._op_runScript.invoke(self, ((scriptID, inputs, waitSecs), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E omero.NoProcessorAvailable: exception ::omero::NoProcessorAvailable E { E serverStackTrace = E serverExceptionClass = E message = No processor available! [0 response(s)] E processorCount = 0 E } ../../../../.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py:935: NoProcessorAvailable ------------------------------ Captured log call ------------------------------- INFO omero.util.Resources:__init__.py:652 Starting INFO omero.processor.ProcessorI:processor.py:814 Registering processor JQ%<\"G`TGkwCx&o#0HY!/UsermodeProcessor-f9d2bfcf-5519-4f50-be4a-a920c30c7899 -t -e 1.1:tcp -h 127.0.0.1 -p 35631 -t 60000 INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4731, group=3686, script=5122 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4731, group=3686, script=5122 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } INFO omero.remote:decorators.py:75 Rslt: INFO omero.remote:decorators.py:75 Rslt: ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4731, group=3686, script=5122 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } INFO omero.remote:decorators.py:75 Rslt: ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4731, group=3686, script=5122 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } INFO omero.remote:decorators.py:75 Rslt: INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept INFO omero.remote:decorators.py:70 Meth: ProcessorI.willAccept ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4731, group=3686, script=5123 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } INFO omero.remote:decorators.py:75 Rslt: ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4731, group=3686, script=5123 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } INFO omero.remote:decorators.py:75 Rslt: ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4731, group=3686, script=5123 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } INFO omero.remote:decorators.py:75 Rslt: ERROR omero.processor.ProcessorI:processor.py:861 File lookup failed: user=4731, group=3686, script=5123 Traceback (most recent call last): File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 857, in willAccept file, handle = self.lookup(scriptContext) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 829, in lookup file = prx.validateScript(job, self.accepts_list) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/processor.py", line 40, in handler return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero_api_IScript_ice.py", line 1065, in validateScript return _M_omero.api.IScript._op_validateScript.invoke(self, ((j, acceptsList), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: Found wrong number of files: [] at ome.services.blitz.impl.ScriptI$15$1.doWork(ScriptI.java:577) at jdk.internal.reflect.GeneratedMethodAccessor265.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.impl.ScriptI$15.call(ScriptI.java:570) at ome.services.throttling.Callback2.run(Callback2.java:43) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:159) at ome.services.blitz.impl.ScriptI.validateScript_async(ScriptI.java:553) at jdk.internal.reflect.GeneratedMethodAccessor656.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy105.validateScript_async(Unknown Source) at omero.api._IScriptTie.validateScript_async(_IScriptTie.java:144) at omero.api._IScriptDisp.___validateScript(_IScriptDisp.java:704) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:819) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = Found wrong number of files: [] } INFO omero.remote:decorators.py:75 Rslt: INFO omero.processor.ProcessorI:__init__.py:597 Cleaning up INFO omero.processor.ProcessorI:__init__.py:599 Done INFO omero.util.Resources:__init__.py:669 Halted _______________ TestThumbnailPerms.testPrivate10618RootWithNoCtx _______________ self = @pytest.mark.broken(reason="requires thumbnail work") def testPrivate10618RootWithNoCtx(self): """ This would require the server to try omero.group=-1 for the user. """ group = self.new_group(perms="rw----") > self.assert10618(group, self.root, True) test/integration/test_thumbnailPerms.py:256: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ test/integration/test_thumbnailPerms.py:217: in assert10618 s = tb_prx.getThumbnailByLongestSideSet(rint(16), [pId], *ctx) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = b185a8ab-1db9-4c67-8824-7052dbcb3e86/f5ea12ea-b748-482d-8d37-6fe1d9c366fbomero.api.ThumbnailStore -t -e 1.1:tcp -h 172.18.0.13 -p 44207 -t 60000 size = object #0 (::omero::RInt) { _val = 16 }, pixelsIds = [2536] _ctx = None def getThumbnailByLongestSideSet(self, size, pixelsIds, _ctx=None): > return _M_omero.api.ThumbnailStore._op_getThumbnailByLongestSideSet.invoke(self, ((size, pixelsIds), _ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E omero.ResourceError: exception ::omero::ResourceError E { E serverStackTrace = ome.conditions.ResourceError: Error retrieving Pixels id:2536. Pixels set does not exist or the user id:0 has insufficient permissions to retrieve it. E at ome.services.ThumbnailCtx.isExtendedGraphCritical(ThumbnailCtx.java:749) E at ome.services.ThumbnailCtx.createAndPrepareMissingRenderingSettings(ThumbnailCtx.java:388) E at ome.services.ThumbnailBean.getThumbnailByLongestSideSet(ThumbnailBean.java:1003) E at jdk.internal.reflect.GeneratedMethodAccessor3850.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.EventHandler.invoke(EventHandler.java:154) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:216) E at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:200) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) E at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) E at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy113.getThumbnailByLongestSideSet(Unknown Source) E at jdk.internal.reflect.GeneratedMethodAccessor3850.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy113.getThumbnailByLongestSideSet(Unknown Source) E at jdk.internal.reflect.GeneratedMethodAccessor3855.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) E at ome.services.throttling.Callback.run(Callback.java:56) E at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) E at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) E at ome.services.blitz.impl.ThumbnailStoreI.getThumbnailByLongestSideSet_async(ThumbnailStoreI.java:83) E at jdk.internal.reflect.GeneratedMethodAccessor3854.invoke(Unknown Source) E at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) E at java.base/java.lang.reflect.Method.invoke(Method.java:566) E at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) E at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) E at omero.cmd.CallContext.invoke(CallContext.java:85) E at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) E at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) E at com.sun.proxy.$Proxy114.getThumbnailByLongestSideSet_async(Unknown Source) E at omero.api._ThumbnailStoreTie.getThumbnailByLongestSideSet_async(_ThumbnailStoreTie.java:132) E at omero.api._ThumbnailStoreDisp.___getThumbnailByLongestSideSet(_ThumbnailStoreDisp.java:743) E at omero.api._ThumbnailStoreDisp.__dispatch(_ThumbnailStoreDisp.java:1088) E at IceInternal.Incoming.invoke(Incoming.java:221) E at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) E at Ice.ConnectionI.dispatch(ConnectionI.java:1145) E at Ice.ConnectionI.message(ConnectionI.java:1056) E at IceInternal.ThreadPool.run(ThreadPool.java:395) E at IceInternal.ThreadPool.access$300(ThreadPool.java:12) E at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) E at java.base/java.lang.Thread.run(Thread.java:829) E E serverExceptionClass = ome.conditions.ResourceError E message = Error retrieving Pixels id:2536. Pixels set does not exist or the user id:0 has insufficient permissions to retrieve it. E } ../../../../.venv3/lib64/python3.11/site-packages/omero_api_ThumbnailStore_ice.py:730: ResourceError ___________________________ TestTickets2000.test1184 ___________________________ self = @pytest.mark.broken(ticket="11543") def test1184(self): uuid = self.uuid() client = self.new_client(perms="rw----") query = client.sf.getQueryService() update = client.sf.getUpdateService() admin = client.sf.getAdminService() cont = client.sf.getContainerService() ds = self.new_dataset(name='test1184-ds-%s' % (uuid)) for i in range(1, 2001): img = self.new_image(name='img1184-%s' % (uuid)) ds.linkImage(img) ds = update.saveAndReturnObject(ds) c = cont.getCollectionCount( ds.__class__.__name__, ("imageLinks"), [ds.id.val], None) assert c[ds.id.val] == 2000 page = 1 p = omero.sys.Parameters() p.map = {} p.map["eid"] = rlong(admin.getEventContext().userId) p.map["oid"] = rlong(ds.id.val) if page is not None: f = omero.sys.Filter() f.limit = rint(24) f.offset = rint((int(page) - 1) * 24) p.theFilter = f sql = "select im from Image im join fetch im.details.owner " \ "join fetch im.details.group left outer join fetch " \ "im.datasetLinks dil left outer join fetch dil.parent d " \ "where d.id = :oid and im.details.owner.id=:eid " \ "order by im.id asc" start = time.time() res = query.findAllByQuery(sql, p) assert 24 == len(res) end = time.time() elapsed = end - start > assert elapsed < 3.0, \ "Expected the test to complete in < 3 seconds, took: %f" % elapsed E AssertionError: Expected the test to complete in < 3 seconds, took: 10.839775 E assert 10.83977484703064 < 3.0 test/integration/test_tickets2000.py:370: AssertionError =============================== warnings summary =============================== OmeroPy/test/integration/clitest/test_import.py::TestImport::testTargetInDifferentGroup[Dataset-test.fake--d] OmeroPy/test/integration/clitest/test_import.py::TestImport::testTargetInDifferentGroup[Screen-SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake--r] /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/plugins/sessions.py:176: DeprecationWarning: OMERO_SESSION_DIR is deprecated. Use OMERO_SESSIONDIR instead. warnings.warn( OmeroPy/test/integration/gatewaytest/test_multi_group.py::TestHistory::testCreateHistory OmeroPy/test/integration/gatewaytest/test_multi_group.py::TestHistory::testCreateHistory OmeroPy/test/integration/gatewaytest/test_multi_group.py::TestScript::testRunScript OmeroPy/test/integration/gatewaytest/test_multi_group.py::TestScript::testRunScript OmeroPy/test/integration/gatewaytest/test_multi_group.py::TestScript::testRunScript /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/gateway/__init__.py:4855: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead logger.warn("%s on %s to <%s> %s(%r, %r)", OmeroPy/test/integration/gatewaytest/test_multi_group.py::TestHistory::testCreateHistory OmeroPy/test/integration/gatewaytest/test_multi_group.py::TestHistory::testCreateHistory OmeroPy/test/integration/gatewaytest/test_multi_group.py::TestScript::testRunScript OmeroPy/test/integration/gatewaytest/test_multi_group.py::TestScript::testRunScript OmeroPy/test/integration/gatewaytest/test_performance.py::TestPerformance::testListFileAnnotations OmeroPy/test/integration/gatewaytest/test_performance.py::TestPerformance::testListFileAnnotations OmeroPy/test/integration/gatewaytest/test_user.py::TestUser::testCrossGroupRead OmeroPy/test/integration/gatewaytest/test_user.py::TestUser::testCrossGroupRead /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/callbacks.py:270: DeprecationWarning: isSet() is deprecated, use is_set() instead return self.event.isSet() OmeroPy/test/integration/scriptstest/test_ping.py::TestPing::testProcessCallback OmeroPy/test/integration/scriptstest/test_ping.py::TestPing::testProcessCallback /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/callbacks.py:89: DeprecationWarning: isSet() is deprecated, use is_set() instead if self.event.isSet(): OmeroPy/test/integration/test_scripts.py::TestScripts::testParamLoadingPerformanceTicket2285 /home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/decorators.py:82: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead log.warn( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html - generated xml file: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroPy/target/reports/broken/junit-results.xml - =========================== short test summary info ============================ FAILED test/integration/clitest/test_fs.py::TestFS::testRenameAdminOnly - AssertionError: assert False + where False = ('SecurityViolation: Admins only!\n') + where = 'disabled since OMERO 5.4.7 due to Pixels.path bug\n'.endswith FAILED test/integration/clitest/test_import.py::TestImport::testTargetInDifferentGroup[Dataset-test.fake--d] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/clitest/test_import.py::TestImport::testTargetInDifferentGroup[Screen-SPW&plates=1&plateRows=1&plateCols=1&fields=1&plateAcqs=1.fake--r] - omero.cli.NonZeroReturnCode: assert failed FAILED test/integration/gatewaytest/test_multi_group.py::TestHistory::testCreateHistory - AssertionError: Logs count should match number of objects assert 1 == 0 FAILED test/integration/gatewaytest/test_multi_group.py::TestScript::testRunScript - omero.NoProcessorAvailable: exception ::omero::NoProcessorAvailable { serverStackTrace = serverExceptionClass = message = No processor available! [0 response(s)] processorCount = 0 } FAILED test/integration/gatewaytest/test_performance.py::TestPerformance::testListFileAnnotations - AssertionError: Blitz listFileAnnotations() should be faster than getObjects('FileAnnotation') assert 0.2187957763671875 < 0.14293193817138672 FAILED test/integration/gatewaytest/test_user.py::TestUser::testCrossGroupRead - assert not 2719 in [2718, 1, 2730, 2719, 2785] + where 2719 = getId() + where getId = <_ExperimenterGroupWrapper id=2719>.getId + and [2718, 1, 2730, 2719, 2785] = object #0 (::omero::sys::EventContext)\n{\n shareId = -1\n sessionId = 10358\n sessionUuid = b45a39b5-81cc-48e6-945f-05bff89a042d\n userId = 3716\n userName = weblitz_test_user\n sudoerId = \n sudoerName = \n groupId = 2718\n groupName = weblitz_test_user_group\n isAdmin = False\n adminPrivileges = \n {\n }\n eventId = -1\n eventType = Internal\n memberOfGroups = \n {\n [0] = 2718\n [1] = 1\n [2] = 2730\n [3] = 2719\n [4] = 2785\n }\n leaderOfGroups = \n {\n }\n groupPermissions = object #1 (::omero::model::Permissions)\n {\n _restrictions = \n {\n }\n _extendedRestrictions = \n {\n }\n _perm1 = -56\n }\n}.memberOfGroups + where object #0 (::omero::sys::EventContext)\n{\n shareId = -1\n sessionId = 10358\n sessionUuid = b45a39b5-81cc-48e6-945f-05bff89a042d\n userId = 3716\n userName = weblitz_test_user\n sudoerId = \n sudoerName = \n groupId = 2718\n groupName = weblitz_test_user_group\n isAdmin = False\n adminPrivileges = \n {\n }\n eventId = -1\n eventType = Internal\n memberOfGroups = \n {\n [0] = 2718\n [1] = 1\n [2] = 2730\n [3] = 2719\n [4] = 2785\n }\n leaderOfGroups = \n {\n }\n groupPermissions = object #1 (::omero::model::Permissions)\n {\n _restrictions = \n {\n }\n _extendedRestrictions = \n {\n }\n _perm1 = -56\n }\n} = getEventContext() + where getEventContext = .getEventContext + where = .gateway FAILED test/integration/scriptstest/test_ping.py::TestPing::testProcessCallback - assert 0 > 0 + where 0 = len([]) + where [] = object #0 (::omero::grid::ProcessCallback)\n{\n}.finish FAILED test/integration/scriptstest/test_repo.py::TestScriptRepo::testGetGroupScripts - assert 6298 in [] FAILED test/integration/tablestest/test_service.py::TestTables::test2098 - AttributeError: type object 'path' has no attribute 'path' FAILED test/integration/tablestest/test_service.py::TestTables::testReadOnlyFile - AttributeError: 'TestTables' object has no attribute 'unique_dir' FAILED test/integration/tablestest/test_service.py::TestTables::testReadEqual - assert [1] == [1, 2, 3, 4, 5] Right contains 4 more items, first extra item: 2 Full diff: [ 1, - 2, - 3, - 4, - 5, ] FAILED test/integration/tablestest/test_service.py::TestTables::testReadOutOfRange - assert [4] == [-1, 0, 1, 2, 3, 4] At index 0 diff: 4 != -1 Right contains 5 more items, first extra item: 0 Full diff: [ - -1, - 0, - 1, - 2, - 3, 4, ] FAILED test/integration/test_admin.py::TestAdmin::testChangePasswordWhenUnset - omero.SecurityViolation: exception ::omero::SecurityViolation { serverStackTrace = ome.conditions.SecurityViolation: Old password is invalid at ome.logic.AdminImpl.changePasswordWithOldPassword(AdminImpl.java:1253) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy91.changePasswordWithOldPassword(Unknown Source) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy91.changePasswordWithOldPassword(Unknown Source) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) at ome.services.blitz.impl.AdminI.changePasswordWithOldPassword_async(AdminI.java:144) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy92.changePasswordWithOldPassword_async(Unknown Source) at omero.api._IAdminTie.changePasswordWithOldPassword_async(_IAdminTie.java:112) at omero.api._IAdminDisp.___changePasswordWithOldPassword(_IAdminDisp.java:1977) at omero.api._IAdminDisp.__dispatch(_IAdminDisp.java:2229) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.SecurityViolation message = Old password is invalid } FAILED test/integration/test_admin.py::TestAdmin::test9193 - omero.ValidationException: exception ::omero::ValidationException { serverStackTrace = ome.conditions.ValidationException: experimenter cannot be a member of only the 'user' group, a different default group is also required at ome.logic.AdminImpl.removeGroups(AdminImpl.java:813) at jdk.internal.reflect.GeneratedMethodAccessor599.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy91.removeGroups(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor599.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy91.removeGroups(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor3194.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) at ome.services.blitz.impl.AdminI.removeGroups_async(AdminI.java:318) at jdk.internal.reflect.GeneratedMethodAccessor3193.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy92.removeGroups_async(Unknown Source) at omero.api._IAdminTie.removeGroups_async(_IAdminTie.java:312) at omero.api._IAdminDisp.___removeGroups(_IAdminDisp.java:1621) at omero.api._IAdminDisp.__dispatch(_IAdminDisp.java:2377) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ValidationException message = experimenter cannot be a member of only the 'user' group, a different default group is also required } FAILED test/integration/test_files.py::TestFiles::testUploadDifferentSizeTicket2337 - omero.OptimisticLockException: exception ::omero::OptimisticLockException { serverStackTrace = ome.conditions.OptimisticLockException: You are not authorized to change the update event for ome.model.core.OriginalFile:Id_6303 from ome.model.meta.Event:Id_123648 to ome.model.meta.Event:Id_123647 You may need to reload the object before continuing. at ome.security.basic.OmeroInterceptor.managedEvent(OmeroInterceptor.java:1201) at ome.security.basic.OmeroInterceptor.checkManagedDetails(OmeroInterceptor.java:963) at ome.security.basic.OmeroInterceptor.resetDetails(OmeroInterceptor.java:465) at ome.security.basic.OmeroInterceptor.onFlushDirty(OmeroInterceptor.java:239) at org.hibernate.event.def.DefaultFlushEntityEventListener.invokeInterceptor(DefaultFlushEntityEventListener.java:372) at org.hibernate.event.def.DefaultFlushEntityEventListener.handleInterception(DefaultFlushEntityEventListener.java:349) at org.hibernate.event.def.DefaultFlushEntityEventListener.scheduleUpdate(DefaultFlushEntityEventListener.java:287) at org.hibernate.event.def.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:155) at org.hibernate.event.def.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:219) at org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:99) at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216) at ome.logic.UpdateImpl.afterUpdate(UpdateImpl.java:342) at ome.logic.UpdateImpl.doAction(UpdateImpl.java:358) at ome.logic.UpdateImpl.doAction(UpdateImpl.java:349) at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:135) at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor1126.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) at ome.services.blitz.impl.UpdateI.saveAndReturnObject_async(UpdateI.java:62) at jdk.internal.reflect.GeneratedMethodAccessor1125.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy95.saveAndReturnObject_async(Unknown Source) at omero.api._IUpdateTie.saveAndReturnObject_async(_IUpdateTie.java:92) at omero.api._IUpdateDisp.___saveAndReturnObject(_IUpdateDisp.java:229) at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:423) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.OptimisticLockException message = You are not authorized to change the update event for ome.model.core.OriginalFile:Id_6303 from ome.model.meta.Event:Id_123648 to ome.model.meta.Event:Id_123647 You may need to reload the object before continuing. backOff = 0 } FAILED test/integration/test_ishare.py::TestIShare::test1172 - assert 0 == 1 + where 0 = len([]) FAILED test/integration/test_itimeline.py::TestITimeline::test1225 - assert 6 == 10 + where 6 = len({1903, 1939, 1990, 9478, 13100, 41436}) FAILED test/integration/test_permissions.py::TestPermissions::test3136 - AssertionError: elapsed1=0.014118432998657227, elapsed2=0.014019012451171875 assert 0.014118432998657227 < (0.1 * 0.014019012451171875) FAILED test/integration/test_permissions.py::TestPermissions::testSaveWithNegOneExplicit - omero.ApiUsageException: exception ::omero::ApiUsageException { serverStackTrace = ome.conditions.ApiUsageException: No valid permissions available! DUMMY permissions are not intended for copying. Make sure that you have not passed omero.group=-1 for a save without context at ome.model.internal.Permissions.(Permissions.java:164) at ome.security.basic.CurrentDetails.createDetails(CurrentDetails.java:439) at ome.security.basic.OmeroInterceptor.newTransientDetails(OmeroInterceptor.java:700) at ome.security.basic.OmeroInterceptor.onSave(OmeroInterceptor.java:187) at org.hibernate.event.def.AbstractSaveEventListener.substituteValuesIfNecessary(AbstractSaveEventListener.java:413) at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:292) at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:203) at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:143) at org.hibernate.event.def.DefaultMergeEventListener.saveTransientEntity(DefaultMergeEventListener.java:415) at org.hibernate.event.def.DefaultMergeEventListener.mergeTransientEntity(DefaultMergeEventListener.java:341) at org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:303) at org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener.entityIsTransient(IdTransferringMergeEventListener.java:62) at ome.security.basic.MergeEventListener.entityIsTransient(MergeEventListener.java:154) at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:258) at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:87) at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:84) at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:73) at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:867) at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:851) at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:855) at ome.logic.UpdateImpl.internalMerge(UpdateImpl.java:313) at ome.logic.UpdateImpl$2.run(UpdateImpl.java:138) at ome.logic.UpdateImpl$2.run(UpdateImpl.java:135) at ome.logic.UpdateImpl.doAction(UpdateImpl.java:357) at ome.logic.UpdateImpl.doAction(UpdateImpl.java:349) at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:135) at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor1126.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) at ome.services.blitz.impl.UpdateI.saveAndReturnObject_async(UpdateI.java:62) at jdk.internal.reflect.GeneratedMethodAccessor1125.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy95.saveAndReturnObject_async(Unknown Source) at omero.api._IUpdateTie.saveAndReturnObject_async(_IUpdateTie.java:92) at omero.api._IUpdateDisp.___saveAndReturnObject(_IUpdateDisp.java:229) at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:423) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ApiUsageException message = No valid permissions available! DUMMY permissions are not intended for copying. Make sure that you have not passed omero.group=-1 for a save without context } FAILED test/integration/test_permissions.py::TestPermissions::testSaveWithNegBadLink - omero.ApiUsageException: exception ::omero::ApiUsageException { serverStackTrace = ome.conditions.ApiUsageException: No valid permissions available! DUMMY permissions are not intended for copying. Make sure that you have not passed omero.group=-1 for a save without context at ome.model.internal.Permissions.(Permissions.java:164) at ome.security.basic.CurrentDetails.createDetails(CurrentDetails.java:439) at ome.security.basic.OmeroInterceptor.newTransientDetails(OmeroInterceptor.java:700) at ome.security.basic.OmeroInterceptor.onSave(OmeroInterceptor.java:187) at org.hibernate.event.def.AbstractSaveEventListener.substituteValuesIfNecessary(AbstractSaveEventListener.java:413) at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:292) at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:203) at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:143) at org.hibernate.event.def.DefaultMergeEventListener.saveTransientEntity(DefaultMergeEventListener.java:415) at org.hibernate.event.def.DefaultMergeEventListener.mergeTransientEntity(DefaultMergeEventListener.java:341) at org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:303) at org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener.entityIsTransient(IdTransferringMergeEventListener.java:62) at ome.security.basic.MergeEventListener.entityIsTransient(MergeEventListener.java:154) at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:258) at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:87) at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:84) at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:73) at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:867) at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:851) at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:855) at ome.logic.UpdateImpl.internalMerge(UpdateImpl.java:313) at ome.logic.UpdateImpl$2.run(UpdateImpl.java:138) at ome.logic.UpdateImpl$2.run(UpdateImpl.java:135) at ome.logic.UpdateImpl.doAction(UpdateImpl.java:357) at ome.logic.UpdateImpl.doAction(UpdateImpl.java:349) at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:135) at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor1126.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) at ome.services.blitz.impl.UpdateI.saveAndReturnObject_async(UpdateI.java:62) at jdk.internal.reflect.GeneratedMethodAccessor1125.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy95.saveAndReturnObject_async(Unknown Source) at omero.api._IUpdateTie.saveAndReturnObject_async(_IUpdateTie.java:92) at omero.api._IUpdateDisp.___saveAndReturnObject(_IUpdateDisp.java:229) at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:423) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ApiUsageException message = No valid permissions available! DUMMY permissions are not intended for copying. Make sure that you have not passed omero.group=-1 for a save without context } FAILED test/integration/test_permissions.py::TestPermissions::testSaveBadLink - omero.SecurityViolation: exception ::omero::SecurityViolation { serverStackTrace = ome.conditions.SecurityViolation: You are not authorized to set the ExperimenterGroup for ome.model.annotations.TagAnnotation:Id_41591 to ome.model.meta.ExperimenterGroup:Id_3681 at ome.security.basic.OmeroInterceptor.newTransientDetails(OmeroInterceptor.java:785) at ome.security.basic.OmeroInterceptor.onSave(OmeroInterceptor.java:187) at org.hibernate.event.def.AbstractSaveEventListener.substituteValuesIfNecessary(AbstractSaveEventListener.java:413) at org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:292) at org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:203) at org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:143) at org.hibernate.event.def.DefaultMergeEventListener.saveTransientEntity(DefaultMergeEventListener.java:415) at org.hibernate.event.def.DefaultMergeEventListener.mergeTransientEntity(DefaultMergeEventListener.java:341) at org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:303) at org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener.entityIsTransient(IdTransferringMergeEventListener.java:62) at ome.security.basic.MergeEventListener.entityIsTransient(MergeEventListener.java:154) at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:258) at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:87) at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:877) at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:859) at org.hibernate.engine.CascadingAction$6.cascade(CascadingAction.java:279) at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:392) at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:335) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204) at org.hibernate.engine.Cascade.cascade(Cascade.java:161) at org.hibernate.event.def.AbstractSaveEventListener.cascadeBeforeSave(AbstractSaveEventListener.java:450) at org.hibernate.event.def.DefaultMergeEventListener.mergeTransientEntity(DefaultMergeEventListener.java:336) at org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:303) at org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener.entityIsTransient(IdTransferringMergeEventListener.java:62) at ome.security.basic.MergeEventListener.entityIsTransient(MergeEventListener.java:154) at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:258) at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:87) at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:877) at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:859) at org.hibernate.engine.CascadingAction$6.cascade(CascadingAction.java:279) at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:392) at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:335) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204) at org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:425) at org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:362) at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:338) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204) at org.hibernate.engine.Cascade.cascade(Cascade.java:161) at org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:475) at org.hibernate.event.def.DefaultMergeEventListener.mergeTransientEntity(DefaultMergeEventListener.java:388) at org.hibernate.event.def.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:303) at org.springframework.orm.hibernate3.support.IdTransferringMergeEventListener.entityIsTransient(IdTransferringMergeEventListener.java:62) at ome.security.basic.MergeEventListener.entityIsTransient(MergeEventListener.java:154) at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:258) at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:87) at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:84) at ome.security.basic.MergeEventListener.onMerge(MergeEventListener.java:73) at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:867) at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:851) at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:855) at ome.logic.UpdateImpl.internalMerge(UpdateImpl.java:313) at ome.logic.UpdateImpl$2.run(UpdateImpl.java:138) at ome.logic.UpdateImpl$2.run(UpdateImpl.java:135) at ome.logic.UpdateImpl.doAction(UpdateImpl.java:357) at ome.logic.UpdateImpl.doAction(UpdateImpl.java:349) at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:135) at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor663.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy94.saveAndReturnObject(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor1126.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) at ome.services.blitz.impl.UpdateI.saveAndReturnObject_async(UpdateI.java:62) at jdk.internal.reflect.GeneratedMethodAccessor1125.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy95.saveAndReturnObject_async(Unknown Source) at omero.api._IUpdateTie.saveAndReturnObject_async(_IUpdateTie.java:92) at omero.api._IUpdateDisp.___saveAndReturnObject(_IUpdateDisp.java:229) at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:423) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.SecurityViolation message = You are not authorized to set the ExperimenterGroup for ome.model.annotations.TagAnnotation:Id_41591 to ome.model.meta.ExperimenterGroup:Id_3681 } FAILED test/integration/test_permissions.py::TestPermissions::testUseOfRawFileBeanScriptReadCorrectGroupAndUser - Ice.UnknownException: exception ::Ice::UnknownException { unknown = ome.conditions.SecurityViolation: User 4726 is not an admin and so cannot set uid to 0 at ome.security.basic.BasicEventContext.checkAndInitialize(BasicEventContext.java:141) at ome.security.basic.CurrentDetails.checkAndInitialize(CurrentDetails.java:317) at ome.security.basic.BasicSecuritySystem.loadEventContext(BasicSecuritySystem.java:449) at ome.security.basic.EventHandler.doLogin(EventHandler.java:210) at ome.security.basic.EventHandler.invoke(EventHandler.java:146) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy74.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.blitz.repo.RepositoryDaoImpl.getFile(RepositoryDaoImpl.java:866) at ome.services.blitz.repo.PublicRepositoryI.checkId(PublicRepositoryI.java:823) at ome.services.blitz.repo.PublicRepositoryI.fileById(PublicRepositoryI.java:367) at omero.grid._RepositoryTie.fileById(_RepositoryTie.java:78) at omero.grid._RepositoryDisp.___fileById(_RepositoryDisp.java:393) at omero.grid._RepositoryDisp.__dispatch(_RepositoryDisp.java:538) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) } FAILED test/integration/test_rawfilestore.py::TestRFS::testTicket1961Basic - AssertionError: assert '' != '' + where '' = object #0 (::omero::RString)\n{\n _val = \n}.val + where object #0 (::omero::RString)\n{\n _val = \n} = object #0 (::omero::model::OriginalFile)\n{\n _id = object #1 (::omero::RLong)\n {\n _val = 6304\n }\n _details = object #2 (::omero::model::Details)\n {\n _owner = object #3 (::omero::model::Experimenter)\n {\n _id = object #4 (::omero::RLong)\n {\n _val = 4727\n }\n _details = \n _loaded = False\n _version = \n _groupExperimenterMapSeq = \n {\n }\n _groupExperimenterMapLoaded = False\n _omeName = \n _firstName = \n _middleName = \n _lastName = \n _institution = \n _ldap = \n _email = \n _config = \n {\n }\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n }\n _group = object #5 (::omero::model::ExperimenterGroup)\n {\n _id = object #6 (::omero::RLong)\n {\n _val = 3683\n }\n _details = object #7 (::... }\n groupPermissions = object #20 (::omero::model::Permissions)\n {\n _restrictions = \n {\n }\n _extendedRestrictions = \n {\n }\n _perm1 = -120\n }\n }\n }\n _loaded = True\n _version = \n _pixelsFileMapsSeq = \n {\n }\n _pixelsFileMapsLoaded = False\n _pixelsFileMapsCountPerOwner = \n {\n }\n _path = object #21 (::omero::RString)\n {\n _val = /tmp/test\n }\n _repo = \n _size = object #22 (::omero::RLong)\n {\n _val = 4\n }\n _atime = \n _mtime = object #23 (::omero::RTime)\n {\n _val = 1765251698327\n }\n _ctime = \n _hasher = \n _hash = object #24 (::omero::RString)\n {\n _val = \n }\n _mimetype = object #25 (::omero::RString)\n {\n _val = application/octet-stream\n }\n _filesetEntriesSeq = \n {\n }\n _filesetEntriesLoaded = True\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n _name = object #26 (::omero::RString)\n {\n _val = test\n }\n}.hash FAILED test/integration/test_rawfilestore.py::TestRFS::testTicket1961WithKillSession - AssertionError: assert '' != '' + where '' = object #0 (::omero::RString)\n{\n _val = \n}.val + where object #0 (::omero::RString)\n{\n _val = \n} = object #0 (::omero::model::OriginalFile)\n{\n _id = object #1 (::omero::RLong)\n {\n _val = 6305\n }\n _details = object #2 (::omero::model::Details)\n {\n _owner = object #3 (::omero::model::Experimenter)\n {\n _id = object #4 (::omero::RLong)\n {\n _val = 4727\n }\n _details = \n _loaded = False\n _version = \n _groupExperimenterMapSeq = \n {\n }\n _groupExperimenterMapLoaded = False\n _omeName = \n _firstName = \n _middleName = \n _lastName = \n _institution = \n _ldap = \n _email = \n _config = \n {\n }\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n }\n _group = object #5 (::omero::model::ExperimenterGroup)\n {\n _id = object #6 (::omero::RLong)\n {\n _val = 3683\n }\n _details = object #7 (::... }\n groupPermissions = object #20 (::omero::model::Permissions)\n {\n _restrictions = \n {\n }\n _extendedRestrictions = \n {\n }\n _perm1 = -120\n }\n }\n }\n _loaded = True\n _version = \n _pixelsFileMapsSeq = \n {\n }\n _pixelsFileMapsLoaded = False\n _pixelsFileMapsCountPerOwner = \n {\n }\n _path = object #21 (::omero::RString)\n {\n _val = /tmp/test\n }\n _repo = \n _size = object #22 (::omero::RLong)\n {\n _val = 4\n }\n _atime = \n _mtime = object #23 (::omero::RTime)\n {\n _val = 1765251698388\n }\n _ctime = \n _hasher = \n _hash = object #24 (::omero::RString)\n {\n _val = \n }\n _mimetype = object #25 (::omero::RString)\n {\n _val = application/octet-stream\n }\n _filesetEntriesSeq = \n {\n }\n _filesetEntriesLoaded = True\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n _name = object #26 (::omero::RString)\n {\n _val = test\n }\n}.hash FAILED test/integration/test_rawfilestore.py::TestRFS::testTicket2161Save - AssertionError: assert '' != '' + where '' = object #0 (::omero::RString)\n{\n _val = \n}.val + where object #0 (::omero::RString)\n{\n _val = \n} = object #0 (::omero::model::OriginalFile)\n{\n _id = object #1 (::omero::RLong)\n {\n _val = 6306\n }\n _details = object #2 (::omero::model::Details)\n {\n _owner = object #3 (::omero::model::Experimenter)\n {\n _id = object #4 (::omero::RLong)\n {\n _val = 4727\n }\n _details = \n _loaded = False\n _version = \n _groupExperimenterMapSeq = \n {\n }\n _groupExperimenterMapLoaded = False\n _omeName = \n _firstName = \n _middleName = \n _lastName = \n _institution = \n _ldap = \n _email = \n _config = \n {\n }\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n }\n _group = object #5 (::omero::model::ExperimenterGroup)\n {\n _id = object #6 (::omero::RLong)\n {\n _val = 3683\n }\n _details = object #7 (::... }\n groupPermissions = object #20 (::omero::model::Permissions)\n {\n _restrictions = \n {\n }\n _extendedRestrictions = \n {\n }\n _perm1 = -120\n }\n }\n }\n _loaded = True\n _version = \n _pixelsFileMapsSeq = \n {\n }\n _pixelsFileMapsLoaded = False\n _pixelsFileMapsCountPerOwner = \n {\n }\n _path = object #21 (::omero::RString)\n {\n _val = /tmp/test\n }\n _repo = \n _size = object #22 (::omero::RLong)\n {\n _val = 4\n }\n _atime = \n _mtime = object #23 (::omero::RTime)\n {\n _val = 1765251698423\n }\n _ctime = \n _hasher = \n _hash = object #24 (::omero::RString)\n {\n _val = \n }\n _mimetype = object #25 (::omero::RString)\n {\n _val = application/octet-stream\n }\n _filesetEntriesSeq = \n {\n }\n _filesetEntriesLoaded = True\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n _name = object #26 (::omero::RString)\n {\n _val = test\n }\n}.hash FAILED test/integration/test_rawfilestore.py::TestRFS::testNoWrite - AssertionError: assert '' != '' + where '' = object #0 (::omero::RString)\n{\n _val = \n}.val + where object #0 (::omero::RString)\n{\n _val = \n} = object #0 (::omero::model::OriginalFile)\n{\n _id = object #1 (::omero::RLong)\n {\n _val = 6307\n }\n _details = object #2 (::omero::model::Details)\n {\n _owner = object #3 (::omero::model::Experimenter)\n {\n _id = object #4 (::omero::RLong)\n {\n _val = 4728\n }\n _details = \n _loaded = False\n _version = \n _groupExperimenterMapSeq = \n {\n }\n _groupExperimenterMapLoaded = False\n _omeName = \n _firstName = \n _middleName = \n _lastName = \n _institution = \n _ldap = \n _email = \n _config = \n {\n }\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n }\n _group = object #5 (::omero::model::ExperimenterGroup)\n {\n _id = object #6 (::omero::RLong)\n {\n _val = 3684\n }\n _details = object #7 (::... }\n groupPermissions = object #20 (::omero::model::Permissions)\n {\n _restrictions = \n {\n }\n _extendedRestrictions = \n {\n }\n _perm1 = -56\n }\n }\n }\n _loaded = True\n _version = \n _pixelsFileMapsSeq = \n {\n }\n _pixelsFileMapsLoaded = False\n _pixelsFileMapsCountPerOwner = \n {\n }\n _path = object #21 (::omero::RString)\n {\n _val = /tmp/test\n }\n _repo = \n _size = object #22 (::omero::RLong)\n {\n _val = 4\n }\n _atime = \n _mtime = object #23 (::omero::RTime)\n {\n _val = 1765251703366\n }\n _ctime = \n _hasher = \n _hash = object #24 (::omero::RString)\n {\n _val = \n }\n _mimetype = object #25 (::omero::RString)\n {\n _val = application/octet-stream\n }\n _filesetEntriesSeq = \n {\n }\n _filesetEntriesLoaded = True\n _annotationLinksSeq = \n {\n }\n _annotationLinksLoaded = False\n _annotationLinksCountPerOwner = \n {\n }\n _name = object #26 (::omero::RString)\n {\n _val = test\n }\n}.hash FAILED test/integration/test_reporawfilestore.py::TestRepoRawFileStore::testFailedWriteNoFile - Failed: DID NOT RAISE FAILED test/integration/test_scripts.py::TestScripts::testAutoFillTicket2326 - omero.NoProcessorAvailable: exception ::omero::NoProcessorAvailable { serverStackTrace = serverExceptionClass = message = No processor available! [0 response(s)] processorCount = 0 } FAILED test/integration/test_scripts.py::TestScripts::testParamLoadingPerformanceTicket2285 - AssertionError: upload_time(0.09987521171569824) <= 10 * params_time(0.6016995906829834)! assert 0.6016995906829834 < (0.09987521171569824 / 10) FAILED test/integration/test_scripts.py::TestScripts::test3527 - omero.NoProcessorAvailable: exception ::omero::NoProcessorAvailable { serverStackTrace = serverExceptionClass = message = No processor available! [0 response(s)] processorCount = 0 } FAILED test/integration/test_thumbnailPerms.py::TestThumbnailPerms::testPrivate10618RootWithNoCtx - omero.ResourceError: exception ::omero::ResourceError { serverStackTrace = ome.conditions.ResourceError: Error retrieving Pixels id:2536. Pixels set does not exist or the user id:0 has insufficient permissions to retrieve it. at ome.services.ThumbnailCtx.isExtendedGraphCritical(ThumbnailCtx.java:749) at ome.services.ThumbnailCtx.createAndPrepareMissingRenderingSettings(ThumbnailCtx.java:388) at ome.services.ThumbnailBean.getThumbnailByLongestSideSet(ThumbnailBean.java:1003) at jdk.internal.reflect.GeneratedMethodAccessor3850.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:216) at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:200) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy113.getThumbnailByLongestSideSet(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor3850.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy113.getThumbnailByLongestSideSet(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor3855.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) at ome.services.throttling.Callback.run(Callback.java:56) at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) at ome.services.blitz.impl.ThumbnailStoreI.getThumbnailByLongestSideSet_async(ThumbnailStoreI.java:83) at jdk.internal.reflect.GeneratedMethodAccessor3854.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy114.getThumbnailByLongestSideSet_async(Unknown Source) at omero.api._ThumbnailStoreTie.getThumbnailByLongestSideSet_async(_ThumbnailStoreTie.java:132) at omero.api._ThumbnailStoreDisp.___getThumbnailByLongestSideSet(_ThumbnailStoreDisp.java:743) at omero.api._ThumbnailStoreDisp.__dispatch(_ThumbnailStoreDisp.java:1088) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ResourceError message = Error retrieving Pixels id:2536. Pixels set does not exist or the user id:0 has insufficient permissions to retrieve it. } FAILED test/integration/test_tickets2000.py::TestTickets2000::test1184 - AssertionError: Expected the test to complete in < 3 seconds, took: 10.839775 assert 10.83977484703064 < 3.0 ==== 33 failed, 3 passed, 2008 deselected, 18 warnings in 182.69s (0:03:02) ==== !! 12/09/25 03:43:12.982 error: 4 communicators not destroyed during global destruction. Result: 1 BUILD SUCCESSFUL Total time: 3 minutes 4 seconds + /home/omero/workspace/OMERO-test-integration/src/build.py -f components/tools/OmeroJava/build.xml -Dtestng.useDefaultListeners=true -Dtestreports.dir=target/reports/broken broken Buildfile: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/build.xml Entering /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava... testng-init: :: Apache Ivy 2.4.0 - 20141213170938 :: http://ant.apache.org/ivy/ :: :: loading settings :: file = /home/omero/workspace/OMERO-test-integration/src/etc/ivysettings.xml 03:43:16,153 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.16 03:43:16,156 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - No custom configurators were discovered as a service. 03:43:16,156 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator 03:43:16,159 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator 03:43:16,160 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] 03:43:16,160 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] 03:43:16,161 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY 03:43:16,161 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator 03:43:16,163 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator 03:43:16,163 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] 03:43:16,163 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes/logback.xml] 03:43:16,164 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@5fffb692 - Resource [logback.xml] occurs multiple times on the classpath. 03:43:16,164 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@5fffb692 - Resource [logback.xml] occurs at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes/logback.xml] 03:43:16,164 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@5fffb692 - Resource [logback.xml] occurs at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated/resources/logback.xml] 03:43:16,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stderr] 03:43:16,363 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] 03:43:16,381 |-INFO in ch.qos.logback.core.model.processor.ImplicitModelHandler - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property 03:43:16,383 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@48cb2d73 - As of version 1.2.0 "immediateFlush" property should be set within the enclosing Appender. 03:43:16,383 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@48cb2d73 - Please move "immediateFlush" property into the enclosing appender. 03:43:16,441 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@48cb2d73 - Setting the "immediateFlush" property of the enclosing appender to true 03:43:16,442 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [velocity] to ERROR 03:43:16,442 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org] to ERROR 03:43:16,442 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [ome] to ERROR 03:43:16,442 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci] to ERROR 03:43:16,442 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to WARN 03:43:16,442 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stderr] to Logger[ROOT] 03:43:16,444 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@243bf087 - End of configuration. 03:43:16,446 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@3086f480 - Registering current configuration as safe fallback point 03:43:16,446 |-INFO in ch.qos.logback.classic.util.ContextInitializer@372461a9 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 283 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY lifecycle.test-compile: Deleting: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/_omero_build_1735069832.tmp Deleting: /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/OmeroJava-test.xml :: loading settings :: file = /home/omero/workspace/OMERO-test-integration/src/etc/ivysettings.xml :: delivering :: omero#OmeroJava-test;working@31657b3efbee :: 5.6.3-576-49aa459db9-ice36-b589-ice36 :: integration :: Tue Dec 09 03:43:13 UTC 2025 delivering ivy file to /home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/OmeroJava-test.xml :: publishing :: omero#OmeroJava-test published OmeroJava-test to /home/omero/workspace/OMERO-test-integration/src/target/test-repository/OmeroJava-test-5.6.3-576-49aa459db9-ice36-b589-ice36.jar published ivy to /home/omero/workspace/OMERO-test-integration/src/target/test-repository/OmeroJava-test-5.6.3-576-49aa459db9-ice36-b589-ice36.xml broken: 03:43:16,948 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.16 03:43:16,951 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - No custom configurators were discovered as a service. 03:43:16,951 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator 03:43:16,952 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator 03:43:16,953 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] 03:43:16,953 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] 03:43:16,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY 03:43:16,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator 03:43:16,954 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator 03:43:16,955 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] 03:43:16,955 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes/logback.xml] 03:43:16,956 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@9f116cc - Resource [logback.xml] occurs multiple times on the classpath. 03:43:16,956 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@9f116cc - Resource [logback.xml] occurs at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/classes/logback.xml] 03:43:16,956 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@9f116cc - Resource [logback.xml] occurs at [file:/home/omero/workspace/OMERO-test-integration/src/components/tools/OmeroJava/target/generated/resources/logback.xml] 03:43:17,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stderr] 03:43:17,129 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] 03:43:17,136 |-INFO in ch.qos.logback.core.model.processor.ImplicitModelHandler - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property 03:43:17,138 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@12468a38 - As of version 1.2.0 "immediateFlush" property should be set within the enclosing Appender. 03:43:17,138 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@12468a38 - Please move "immediateFlush" property into the enclosing appender. 03:43:17,161 |-WARN in ch.qos.logback.classic.encoder.PatternLayoutEncoder@12468a38 - Setting the "immediateFlush" property of the enclosing appender to true 03:43:17,161 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [velocity] to ERROR 03:43:17,161 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org] to ERROR 03:43:17,161 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [ome] to ERROR 03:43:17,161 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci] to ERROR 03:43:17,161 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to WARN 03:43:17,161 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stderr] to Logger[ROOT] 03:43:17,162 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1aa7ecca - End of configuration. 03:43:17,162 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@59309333 - Registering current configuration as safe fallback point 03:43:17,162 |-INFO in ch.qos.logback.classic.util.ContextInitializer@67d48005 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 208 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY =============================================== OmeroJava.integration Total tests run: 43, Passes: 2, Failures: 41, Skips: 0 =============================================== The tests failed. BUILD SUCCESSFUL Total time: 1 minute 34 seconds + deactivate + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']' + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin + export PATH + unset _OLD_VIRTUAL_PATH + '[' -n '' ']' + hash -r + '[' -n '' ']' + unset VIRTUAL_ENV + unset VIRTUAL_ENV_PROMPT + '[' '!' '' = nondestructive ']' + unset -f deactivate Recording test results [Checks API] No suitable checks publisher found. Build step 'Publish JUnit test result report' changed build result to UNSTABLE TestNG Reports Processing: START Looking for TestNG results report in workspace using pattern: **/OmeroJava/target/reports/integration/*.xml Saving reports... Processing '/var/jenkins_home/jobs/OMERO-test-integration/builds/554/testng/testng-results-1.xml' Processing '/var/jenkins_home/jobs/OMERO-test-integration/builds/554/testng/testng-results.xml' 0.386250% of tests failed, which exceeded threshold of 0%. Marking build as UNSTABLE TestNG Reports Processing: FINISH Finished: UNSTABLE