Started by upstream project "Trigger" build number 25
originally caused by:
 Started by timer
Running as SYSTEM
Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
[OMERO-server] $ /bin/bash -xe /tmp/jenkins5768161282569314361.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-server
+ OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
+ export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
+ OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
+ OMERO_DATA_DIR=/home/omero/omero-server-data
+ '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
+ source /home/omero/workspace/OMERO-server/.venv3/bin/activate
++ deactivate nondestructive
++ '[' -n '' ']'
++ '[' -n '' ']'
++ '[' -n /bin/bash -o -n '' ']'
++ hash -r
++ '[' -n '' ']'
++ unset VIRTUAL_ENV
++ '[' '!' nondestructive = nondestructive ']'
++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.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-server/.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
++ '[' -n /bin/bash -o -n '' ']'
++ hash -r
+ omero admin stop
Server not running
+ echo not running
not running
+ sleep 5
+ 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 '' ']'
+ '[' -n /bin/bash -o -n '' ']'
+ hash -r
+ '[' -n '' ']'
+ unset VIRTUAL_ENV
+ '[' '!' '' = nondestructive ']'
+ unset -f deactivate
+ rm -rf /home/omero/workspace/OMERO-server/.venv3
+ python3 -m venv /home/omero/workspace/OMERO-server/.venv3
+ '[' false = true ']'
+ echo 'Skipping PURGE_DATA:CleanDbAndRepo'
Skipping PURGE_DATA:CleanDbAndRepo
+ rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.7.3-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero-dropbox-5.6.3.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero-py-5.19.2.dev0.tar.gz /home/omero/workspace/OMERO-server/omero-scripts-5.8.1.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero-web-5.25.1.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
Copied 1 artifact from "OMERO-build" build number 22
Copied 5 artifacts from "OMERO-python-superbuild-build" build number 22
Copied 2 artifacts from "OMERO-build-build" build number 22
[OMERO-server] $ /bin/bash -xe /tmp/jenkins15166408914255984486.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-server
+ OMERO_DATA_DIR=/home/omero/omero-server-data
+ mkdir -p /home/omero/omero-server-data
+ OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
+ export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
+ OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
+ export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
+ ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
+ export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
+ VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
++ ls OMERO.server-5.6.3-450-02d2190d74-ice36.zip
+ ZIP=OMERO.server-5.6.3-450-02d2190d74-ice36.zip
+ '[' '!' -z '' ']'
+ DIST=OMERO.server-5.6.3-450-02d2190d74-ice36
+ unzip OMERO.server-5.6.3-450-02d2190d74-ice36.zip
Archive:  OMERO.server-5.6.3-450-02d2190d74-ice36.zip
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  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/cpl-v10.html  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/crystalclear.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/django.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/dom4j.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/epl-v1.0.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/fbsd.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/freemarker.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/gpl-v2.0.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/gpl.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/gtest.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/iconsweets_license.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/jamon.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/jmock.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/jquery.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/jtidy.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/lgpl-3.0.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/lgpl-v2.0.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/lgpl-v2.1.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/lgpl-v3.0.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/lgpl.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/matplotlib.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/mit.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/mpl-v1_0.htm  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/npl-1_1.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/path.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/pil.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/postgresql.txt  
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  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/scons.txt  
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  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/share/licenses/zpl-v2.1.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/sql/README.txt  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/sql/misc/Makefile  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/sql/misc/current.sql  
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  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/sql/psql/OMERO3A__10/OMERO3A__9.sql  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/sql/psql/OMERO3A__11/OMERO3A__10.sql  
  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/sql/psql/OMERO3A__11/OMERO3A__5.sql  
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  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py  
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  inflating: OMERO.server-5.6.3-450-02d2190d74-ice36/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql  
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+ rm -f OMERO.server-5.6.3-450-02d2190d74-ice36.zip
+ mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-450-02d2190d74-ice36 /home/omero/workspace/OMERO-server/OMERO.server
+ source /home/omero/workspace/OMERO-server/.venv3/bin/activate
++ deactivate nondestructive
++ '[' -n '' ']'
++ '[' -n '' ']'
++ '[' -n /bin/bash -o -n '' ']'
++ hash -r
++ '[' -n '' ']'
++ unset VIRTUAL_ENV
++ '[' '!' nondestructive = nondestructive ']'
++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.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-server/.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
++ '[' -n /bin/bash -o -n '' ']'
++ hash -r
+ pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl
Collecting zeroc-ice==3.6.5
  Downloading https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl (31.3 MB)
Installing collected packages: zeroc-ice
Successfully installed zeroc-ice-3.6.5
+ pip install -U pip future
Requirement already satisfied: pip in ./.venv3/lib/python3.9/site-packages (21.2.3)
Collecting pip
  Using cached pip-24.0-py3-none-any.whl (2.1 MB)
Collecting future
  Using cached future-1.0.0-py3-none-any.whl (491 kB)
Installing collected packages: pip, future
  Attempting uninstall: pip
    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
      Successfully uninstalled pip-21.2.3
Successfully installed future-1.0.0 pip-24.0
+ pip install markdown
Collecting markdown
  Using cached Markdown-3.6-py3-none-any.whl.metadata (7.0 kB)
Collecting importlib-metadata>=4.4 (from markdown)
  Using cached importlib_metadata-7.1.0-py3-none-any.whl.metadata (4.7 kB)
Collecting zipp>=0.5 (from importlib-metadata>=4.4->markdown)
  Using cached zipp-3.18.1-py3-none-any.whl.metadata (3.5 kB)
Using cached Markdown-3.6-py3-none-any.whl (105 kB)
Using cached importlib_metadata-7.1.0-py3-none-any.whl (24 kB)
Using cached zipp-3.18.1-py3-none-any.whl (8.2 kB)
Installing collected packages: zipp, importlib-metadata, markdown
Successfully installed importlib-metadata-7.1.0 markdown-3.6 zipp-3.18.1
+ pip install reportlab
Collecting reportlab
  Using cached reportlab-4.1.0-py3-none-any.whl.metadata (1.4 kB)
Collecting pillow>=9.0.0 (from reportlab)
  Using cached pillow-10.3.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.2 kB)
Collecting chardet (from reportlab)
  Using cached chardet-5.2.0-py3-none-any.whl.metadata (3.4 kB)
Using cached reportlab-4.1.0-py3-none-any.whl (1.9 MB)
Using cached pillow-10.3.0-cp39-cp39-manylinux_2_28_x86_64.whl (4.5 MB)
Using cached chardet-5.2.0-py3-none-any.whl (199 kB)
Installing collected packages: pillow, chardet, reportlab
Successfully installed chardet-5.2.0 pillow-10.3.0 reportlab-4.1.0
+ pip install omego
Collecting omego
  Using cached omego-0.7.0-py3-none-any.whl
Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omego) (1.0.0)
Collecting yaclifw>=0.1.1 (from omego)
  Using cached yaclifw-0.2.0-py3-none-any.whl
Collecting six (from yaclifw>=0.1.1->omego)
  Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Installing collected packages: six, yaclifw, omego
Successfully installed omego-0.7.0 six-1.16.0 yaclifw-0.2.0
+ pip install tables
Collecting tables
  Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
Collecting numpy>=1.19.0 (from tables)
  Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting numexpr>=2.6.2 (from tables)
  Using cached numexpr-2.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.9 kB)
Collecting packaging (from tables)
  Using cached packaging-24.0-py3-none-any.whl.metadata (3.2 kB)
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 blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.2 kB)
Collecting ndindex>=1.4 (from blosc2>=2.3.0->tables)
  Using cached ndindex-1.8-py3-none-any.whl.metadata (3.4 kB)
Collecting msgpack (from blosc2>=2.3.0->tables)
  Using cached msgpack-1.0.8-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.1 kB)
Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
Using cached numexpr-2.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (375 kB)
Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
Using cached packaging-24.0-py3-none-any.whl (53 kB)
Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
Using cached ndindex-1.8-py3-none-any.whl (91 kB)
Using cached msgpack-1.0.8-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (385 kB)
Installing collected packages: py-cpuinfo, packaging, numpy, ndindex, msgpack, numexpr, blosc2, tables
Successfully installed blosc2-2.5.1 msgpack-1.0.8 ndindex-1.8 numexpr-2.10.0 numpy-1.26.4 packaging-24.0 py-cpuinfo-9.0.0 tables-3.9.2
+ pip install jinja2
Collecting jinja2
  Using cached Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
Collecting MarkupSafe>=2.0 (from jinja2)
  Using cached MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Using cached Jinja2-3.1.3-py3-none-any.whl (133 kB)
Using cached MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Installing collected packages: MarkupSafe, jinja2
Successfully installed MarkupSafe-2.1.5 jinja2-3.1.3
+ pip install omero-py
Collecting omero-py
  Using cached omero_py-5.19.1-py3-none-any.whl.metadata (6.6 kB)
Collecting urllib3<2 (from omero-py)
  Using cached urllib3-1.26.18-py2.py3-none-any.whl.metadata (48 kB)
Collecting appdirs (from omero-py)
  Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py) (1.0.0)
Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py) (1.26.4)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py) (10.3.0)
Collecting PyYAML (from omero-py)
  Using cached PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py) (3.6.5)
Collecting requests (from omero-py)
  Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting portalocker (from omero-py)
  Using cached portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB)
Collecting charset-normalizer<4,>=2 (from requests->omero-py)
  Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests->omero-py)
  Using cached idna-3.6-py3-none-any.whl.metadata (9.9 kB)
Collecting certifi>=2017.4.17 (from requests->omero-py)
  Using cached certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
Using cached omero_py-5.19.1-py3-none-any.whl (2.8 MB)
Using cached urllib3-1.26.18-py2.py3-none-any.whl (143 kB)
Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Using cached portalocker-2.8.2-py3-none-any.whl (17 kB)
Using cached PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB)
Using cached requests-2.31.0-py3-none-any.whl (62 kB)
Using cached certifi-2024.2.2-py3-none-any.whl (163 kB)
Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB)
Using cached idna-3.6-py3-none-any.whl (61 kB)
Installing collected packages: appdirs, urllib3, PyYAML, portalocker, idna, charset-normalizer, certifi, requests, omero-py
Successfully installed PyYAML-6.0.1 appdirs-1.4.4 certifi-2024.2.2 charset-normalizer-3.3.2 idna-3.6 omero-py-5.19.1 portalocker-2.8.2 requests-2.31.0 urllib3-1.26.18
+ pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
Collecting omero-metadata
  Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-a2t4b2kt/omero-metadata_79507be448fe423ca846a615d43281f1
  Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-a2t4b2kt/omero-metadata_79507be448fe423ca846a615d43281f1
  Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 1001c4a2e45f9607bae5cc98bea4620173e1e981
  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'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (5.19.1)
Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (6.0.1)
Requirement already satisfied: jinja2 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (3.1.3)
Collecting pandas (from omero-metadata)
  Using cached pandas-2.2.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.18)
Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.4)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (10.3.0)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.31.0)
Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.8.2)
Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib/python3.9/site-packages (from jinja2->omero-metadata) (2.1.5)
Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas->omero-metadata)
  Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas->omero-metadata)
  Using cached tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB)
Requirement already satisfied: six>=1.5 in ./.venv3/lib/python3.9/site-packages (from python-dateutil>=2.8.2->pandas->omero-metadata) (1.16.0)
Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.6)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2024.2.2)
Using cached pandas-2.2.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.0 MB)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB)
Using cached tzdata-2024.1-py2.py3-none-any.whl (345 kB)
Building wheels for collected packages: omero-metadata
  Building wheel for omero-metadata (pyproject.toml): started
  Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
  Created wheel for omero-metadata: filename=omero_metadata-0.12.1.dev0-py3-none-any.whl size=39111 sha256=7e0b198d5b94ea2006186f48b2233c81abd60dc741c652130b265eeb7db43c2c
  Stored in directory: /tmp/pip-ephem-wheel-cache-85ea00d9/wheels/64/09/47/3b86b706f8f6f4bec1b7fd6641d2e4a09814e754fa4c85c82d
Successfully built omero-metadata
Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
Successfully installed omero-metadata-0.12.1.dev0 pandas-2.2.1 python-dateutil-2.9.0.post0 pytz-2024.1 tzdata-2024.1
+ pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
Collecting omero-cli-render
  Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-lmlpatie/omero-cli-render_c7203eff221b4fc0a54cbd4c9bf17a80
  Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-lmlpatie/omero-cli-render_c7203eff221b4fc0a54cbd4c9bf17a80
  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-render.git to commit 3b7890f3181bbefff8b7c55075f677da4fb6bc5c
  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'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (6.0.1)
Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (5.19.1)
Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (1.0.0)
Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.18)
Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.4)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (10.3.0)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.31.0)
Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.8.2)
Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.6)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2024.2.2)
Building wheels for collected packages: omero-cli-render
  Building wheel for omero-cli-render (pyproject.toml): started
  Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
  Created wheel for omero-cli-render: filename=omero_cli_render-0.8.1.dev0-py3-none-any.whl size=18018 sha256=765da61d63eae1b16aa2ed6b9f00d520b37123f91d412c7683a949f6511b488d
  Stored in directory: /tmp/pip-ephem-wheel-cache-srde75cs/wheels/58/32/1b/746489b3c7c17a98c6cd7195bdd3b426dd4137caeb1045a994
Successfully built omero-cli-render
Installing collected packages: omero-cli-render
Successfully installed omero-cli-render-0.8.1.dev0
+ 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-skmgu952/omero-cli-duplicate_19c093f494b5407582496cc7511cd3f7
  Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-skmgu952/omero-cli-duplicate_19c093f494b5407582496cc7511cd3f7
  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 4a8613b78be26812867c0357af6ccbf11269eb6e
  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'
  Installing backend dependencies: started
  Installing backend dependencies: 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/lib/python3.9/site-packages (from omero-cli-duplicate) (5.19.1)
Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.18)
Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.4)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (10.3.0)
Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.1)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.31.0)
Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.8.2)
Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.6)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2024.2.2)
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=11443 sha256=9e363c842ecfa8f531aae0d673227bc9369f301f8b6d75af23906af30e4f41a6
  Stored in directory: /tmp/pip-ephem-wheel-cache-fh8licl5/wheels/f1/55/ac/0cb8b093a4c417e5157143839711e7613efa64eaa21c29ef84
Successfully built omero-cli-duplicate
Installing collected packages: omero-cli-duplicate
Successfully installed omero-cli-duplicate-0.4.1.dev0
+ pip install omero-certificates
Collecting omero-certificates
  Using cached omero_certificates-0.3.2-py3-none-any.whl.metadata (3.7 kB)
Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-certificates) (5.19.1)
Collecting distro==1.8.0 (from omero-certificates)
  Using cached distro-1.8.0-py3-none-any.whl.metadata (6.9 kB)
Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.18)
Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.4)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (10.3.0)
Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.1)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.31.0)
Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.8.2)
Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.6)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2024.2.2)
Using cached omero_certificates-0.3.2-py3-none-any.whl (13 kB)
Using cached distro-1.8.0-py3-none-any.whl (20 kB)
Installing collected packages: distro, omero-certificates
Successfully installed distro-1.8.0 omero-certificates-0.3.2
+ for x in *.tar.gz
+ pip install -U omero-dropbox-5.6.3.dev0.tar.gz
Processing ./omero-dropbox-5.6.3.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'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: omero-py in ./.venv3/lib/python3.9/site-packages (from omero-dropbox==5.6.3.dev0) (5.19.1)
Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (1.26.18)
Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (1.0.0)
Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (1.26.4)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (10.3.0)
Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (6.0.1)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (2.31.0)
Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (2.8.2)
Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.6.3.dev0) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.6.3.dev0) (3.6)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.6.3.dev0) (2024.2.2)
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-5.6.3.dev0-py3-none-any.whl size=49057 sha256=eb6aeece1edfc703b16bf42104c636d8d74cc7ea85b5e004dc7686758500bd5d
  Stored in directory: /home/omero/.cache/pip/wheels/a5/63/29/4452e52704e5ad491f397a0013b20ebb9d413ceb110f8101d1
Successfully built omero-dropbox
Installing collected packages: omero-dropbox
Successfully installed omero-dropbox-5.6.3.dev0
+ for x in *.tar.gz
+ pip install -U omero_marshal-0.9.1.dev0.tar.gz
Processing ./omero_marshal-0.9.1.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'
  Installing backend dependencies: started
  Installing backend dependencies: 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-0.9.1.dev0-py3-none-any.whl size=88031 sha256=5af1ece70b691a357afbbe7acbf53818643d0bac781db3ce633f5ff95c495c96
  Stored in directory: /home/omero/.cache/pip/wheels/8b/40/f1/dbed071eff57c96e0824ead2a420a7a1a080f7fbdfe0431d7f
Successfully built omero_marshal
Installing collected packages: omero_marshal
Successfully installed omero_marshal-0.9.1.dev0
+ for x in *.tar.gz
+ pip install -U omero-py-5.19.2.dev0.tar.gz
Processing ./omero-py-5.19.2.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'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.2.dev0) (1.26.18)
Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.2.dev0) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.2.dev0) (1.0.0)
Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.2.dev0) (1.26.4)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.2.dev0) (10.3.0)
Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.2.dev0) (6.0.1)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.2.dev0) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.2.dev0) (2.31.0)
Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.2.dev0) (2.8.2)
Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.2.dev0) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.2.dev0) (3.6)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.2.dev0) (2024.2.2)
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-5.19.2.dev0-py3-none-any.whl size=2781994 sha256=8a59402beb9cd5f33356e530ed499319b4a100e109ea3fd8104dd09ee8dc1f5a
  Stored in directory: /home/omero/.cache/pip/wheels/9c/89/be/2493ce5a19b07550997c567708af9d7056cfee1f4f39ac699d
Successfully built omero-py
Installing collected packages: omero-py
  Attempting uninstall: omero-py
    Found existing installation: omero-py 5.19.1
    Uninstalling omero-py-5.19.1:
      Successfully uninstalled omero-py-5.19.1
Successfully installed omero-py-5.19.2.dev0
+ for x in *.tar.gz
+ pip install -U omero-scripts-5.8.1.dev0.tar.gz
Processing ./omero-scripts-5.8.1.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'
  Installing backend dependencies: started
  Installing backend dependencies: 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-5.8.1.dev0-py3-none-any.whl size=116570 sha256=74aab0f5e980251bab682d3054c63497b835c7cbeb32671591cfa983016e4414
  Stored in directory: /home/omero/.cache/pip/wheels/ef/a0/80/e3393129cedc64a3ad2b8c2fa437d83a3d318cba65d425f5cf
Successfully built omero-scripts
Installing collected packages: omero-scripts
Successfully installed omero-scripts-5.8.1.dev0
+ for x in *.tar.gz
+ pip install -U omero-web-5.25.1.dev0.tar.gz
Processing ./omero-web-5.25.1.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'
  Installing backend dependencies: started
  Installing backend dependencies: 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/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (5.19.2.dev0)
Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.25.1.dev0)
  Using cached concurrent_log_handler-0.9.25-py3-none-any.whl.metadata (17 kB)
Collecting Django<4.3,>=4.2.3 (from omero-web==5.25.1.dev0)
  Using cached Django-4.2.11-py3-none-any.whl.metadata (4.2 kB)
Collecting django-pipeline==2.1.0 (from omero-web==5.25.1.dev0)
  Using cached django_pipeline-2.1.0-py3-none-any.whl.metadata (12 kB)
Collecting django-cors-headers==3.7.0 (from omero-web==5.25.1.dev0)
  Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
Collecting django-csp (from omero-web==5.25.1.dev0)
  Using cached django_csp-3.8-py3-none-any.whl.metadata (2.7 kB)
Collecting whitenoise>=5.3.0 (from omero-web==5.25.1.dev0)
  Using cached whitenoise-6.6.0-py3-none-any.whl.metadata (3.7 kB)
Collecting gunicorn>=19.3 (from omero-web==5.25.1.dev0)
  Using cached gunicorn-21.2.0-py3-none-any.whl.metadata (4.1 kB)
Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (0.9.1.dev0)
Requirement already satisfied: Pillow in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (10.3.0)
Requirement already satisfied: pytz in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (2024.1)
Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (2.8.2)
Requirement already satisfied: packaging in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (24.0)
Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.25.1.dev0)
  Using cached asgiref-3.8.1-py3-none-any.whl.metadata (9.3 kB)
Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.25.1.dev0)
  Using cached sqlparse-0.4.4-py3-none-any.whl.metadata (4.0 kB)
Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (1.26.18)
Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (1.0.0)
Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (1.26.4)
Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (6.0.1)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (2.31.0)
Collecting typing-extensions>=4 (from asgiref<4,>=3.6.0->Django<4.3,>=4.2.3->omero-web==5.25.1.dev0)
  Using cached typing_extensions-4.10.0-py3-none-any.whl.metadata (3.0 kB)
Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.25.1.dev0) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.25.1.dev0) (3.6)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.25.1.dev0) (2024.2.2)
Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
Using cached django_pipeline-2.1.0-py3-none-any.whl (38 kB)
Using cached concurrent_log_handler-0.9.25-py3-none-any.whl (25 kB)
Using cached Django-4.2.11-py3-none-any.whl (8.0 MB)
Using cached gunicorn-21.2.0-py3-none-any.whl (80 kB)
Using cached whitenoise-6.6.0-py3-none-any.whl (19 kB)
Using cached django_csp-3.8-py3-none-any.whl (17 kB)
Using cached asgiref-3.8.1-py3-none-any.whl (23 kB)
Using cached sqlparse-0.4.4-py3-none-any.whl (41 kB)
Using cached typing_extensions-4.10.0-py3-none-any.whl (33 kB)
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-5.25.1.dev0-py3-none-any.whl size=2770069 sha256=c7a1d01db08a70db51040384d262932ae619b69ad7a11a5238fd20eaaca5cf6a
  Stored in directory: /home/omero/.cache/pip/wheels/c5/4f/aa/011f4ecfdcda915571d213b068a736fbddf1b36b2e590de11a
Successfully built omero-web
Installing collected packages: django-pipeline, whitenoise, typing-extensions, sqlparse, gunicorn, concurrent-log-handler, asgiref, Django, django-csp, django-cors-headers, omero-web
Successfully installed Django-4.2.11 asgiref-3.8.1 concurrent-log-handler-0.9.25 django-cors-headers-3.7.0 django-csp-3.8 django-pipeline-2.1.0 gunicorn-21.2.0 omero-web-5.25.1.dev0 sqlparse-0.4.4 typing-extensions-4.10.0 whitenoise-6.6.0
+ wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
--2024-04-04 00:46:54--  https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.109.133, 185.199.108.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 94614 (92K) [text/plain]
Saving to: ‘Figure_To_Pdf.py’

     0K .......... .......... .......... .......... .......... 54% 2.47M 0s
    50K .......... .......... .......... .......... ..        100% 8.59M=0.02s

2024-04-04 00:46:55 (3.68 MB/s) - ‘Figure_To_Pdf.py’ saved [94614/94614]

+ chmod 755 Figure_To_Pdf.py
+ mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
+ omero config set omero.db.name OMERO-server
+ omero config set omero.db.host pg
+ omero config set omero.db.user postgres
+ omero config set omero.data.dir /home/omero/omero-server-data
+ omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
+ omero config set omero.db.poolsize 25
+ omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
+ omero config set omero.security.trustStorePassword changeit
+ omero config set omero.mail.config true
+ omero config set omero.mail.from qa@openmicroscopy.org.uk
+ omero config set omero.mail.host smtp.dundee.ac.uk
+ omero certificates
OpenSSL 3.0.7 1 Nov 2022 (Library: OpenSSL 3.0.7 1 Nov 2022)
certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
+ '[' false = true ']'
+ echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
+ omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
2024-04-04 00:47:17,106 [    omego.db] DEBUG            dbcommand => upgrade
2024-04-04 00:47:17,106 [    omego.db] DEBUG               dbhost => localhost
2024-04-04 00:47:17,106 [    omego.db] DEBUG               dbname => OMERO-server
2024-04-04 00:47:17,106 [    omego.db] DEBUG               dbpass => omero
2024-04-04 00:47:17,106 [    omego.db] DEBUG               dbuser => omero
2024-04-04 00:47:17,106 [    omego.db] DEBUG             rootpass => omero
2024-04-04 00:47:17,106 [    omego.db] DEBUG            serverdir => /home/omero/workspace/OMERO-server/OMERO.server
2024-04-04 00:47:17,106 [omego.extern] INFO  Executing : omero version
OMERO.py version:
OMERO.server version:
5.6.3-450-02d2190d74-ice36
5.19.2.dev0
2024-04-04 00:47:19,137 [omego.extern] INFO  Completed [2.030 s]
2024-04-04 00:47:19,137 [omego.extern] DEBUG Using omero CLI from omero
2024-04-04 00:47:19,137 [    omego.db] INFO  DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
2024-04-04 00:47:19,138 [omego.extern] INFO  Running [current environment]: omero config get --show-password
2024-04-04 00:47:19,138 [omego.extern] INFO  Executing : omero config get --show-password
2024-04-04 00:47:21,033 [omego.extern] INFO  Completed [1.895 s]
2024-04-04 00:47:21,033 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
2024-04-04 00:47:21,033 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
2024-04-04 00:47:21,090 [omego.extern] INFO  Completed [0.057 s]
2024-04-04 00:47:21,090 [    omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.2\n'
2024-04-04 00:47:21,091 [    omego.db] INFO  psql version: psql (PostgreSQL) 16.2

2024-04-04 00:47:21,091 [omego.extern] INFO  Running [current environment]: omero config get --show-password
2024-04-04 00:47:21,091 [omego.extern] INFO  Executing : omero config get --show-password
2024-04-04 00:47:22,660 [omego.extern] INFO  Completed [1.569 s]
2024-04-04 00:47:22,661 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
2024-04-04 00:47:22,661 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
2024-04-04 00:47:22,814 [omego.extern] INFO  Completed [0.153 s]
2024-04-04 00:47:22,814 [    omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.7") at port "5432".\n'
2024-04-04 00:47:22,815 [    omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
2024-04-04 00:47:22,815 [omego.extern] INFO  Running [current environment]: omero config get --show-password
2024-04-04 00:47:22,815 [omego.extern] INFO  Executing : omero config get --show-password
2024-04-04 00:47:24,571 [omego.extern] INFO  Completed [1.756 s]
2024-04-04 00:47:24,571 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
2024-04-04 00:47:24,572 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
2024-04-04 00:47:24,994 [omego.extern] INFO  Completed [0.423 s]
2024-04-04 00:47:24,995 [    omego.db] DEBUG stdout: b'OMERO5.4|0\n'
2024-04-04 00:47:24,995 [    omego.db] INFO  Current omero db version: ('OMERO5.4', '0')
2024-04-04 00:47:24,998 [    omego.db] INFO  Database is already at OMERO5.4__0
+ export LANG=en_US.UTF-8
+ LANG=en_US.UTF-8
+ export LANGUAGE=en_US:en
+ LANGUAGE=en_US:en
+ export LC_ALL=en_US.UTF-8
+ LC_ALL=en_US.UTF-8
+ BUILD_ID=DONT_KILL_ME
+ omero admin start
WARNING: lock files in /home/omero/omero-server-data
----------------------------------------
/home/omero/omero-server-data/.omero/repository/7097ab62-1c9f-4ba2-a5e5-d5b1f868081e/.lock
----------------------------------------

You may want to stop all server processes and remove
these files manually. Lock files can remain after an
abrupt server outage and are especially frequent on
remotely mounted filesystems like NFS.

No descriptor given. Using etc/grid/default.xml
Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
Creating /home/omero/workspace/OMERO-server/OMERO.server/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                  11.0.22   (/usr/bin/java)
Commands:   python -V                      3.9.18    (/home/omero/workspace/OMERO-server/.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                 16.2      (/usr/bin/psql)
Commands:   openssl version                3.0.71    (/usr/bin/openssl)

Component:  OMERO.py                       5.19.2.dev0
Component:  OMERO.server                   5.6.3-450-02d2190d74-ice36

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 2661, enabled)
Server:     DropBox                        active (pid = 2685, enabled)
Server:     FileServer                     active (pid = 2692, enabled)
Server:     Indexer-0                      activating (enabled)
Server:     MonitorServer                  active (pid = 2693, enabled)
Server:     OMERO.Glacier2                 active (pid = 2717, enabled)
Server:     OMERO.IceStorm                 active (pid = 2695, 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-server/OMERO.server/var/log exists
Log files:  Blitz-0.log                    25.3 KB       errors=0    warnings=1   
Log files:  DropBox.log                    1.2 KB       
Log files:  FileServer.log                 114 B        
Log files:  Indexer-0.log                  2.0 KB       
Log files:  MonitorServer.log              1.1 KB       
Log files:  PixelData-0.log                1.6 KB       
Log files:  Processor-0.log                592 B        
Log files:  Tables-0.log                   841 B        
Log files:  TestDropBox.log                n/a
Log files:  master.err                     2.1 KB       
Log files:  master.out                     41.5 KB      
Log files:  Total size                     0.08 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)          
Environment:OMERO_TMPDIR=(unset)           
Environment:PATH=/home/omero/workspace/OMERO-server/.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:4064                           
OMERO TCP port:4063                           
OMERO data dir:'/home/omero/omero-server-data' Exists? True	Is writable? True
OMERO temp dir:'/home/omero/omero/tmp'        Exists? True	Is writable? True   (Size: 0)

JVM settings: Blitz-${index}                -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

Jar:        lib/server/formats-api.jar     Bio-Formats API	8.0.0-SNAPSHOT	4 April 2024	ee958be196493eebf99c7ed204dc9356eb2f8327
Jar:        lib/server/formats-bsd.jar     BSD Bio-Formats readers and writers	8.0.0-SNAPSHOT	4 April 2024	ee958be196493eebf99c7ed204dc9356eb2f8327
Jar:        lib/server/formats-gpl.jar     Bio-Formats library	8.0.0-SNAPSHOT	4 April 2024	ee958be196493eebf99c7ed204dc9356eb2f8327
Jar:        lib/server/ome-codecs.jar      OME Codecs	1.0.2-SNAPSHOT	4 April 2024	94f975dfe39c34c8c39668ad0b0f54974375920e
Jar:        lib/server/ome-common.jar      OME Common Java	6.0.22-SNAPSHOT	4 April 2024	94f975dfe39c34c8c39668ad0b0f54974375920e
Jar:        lib/server/ome-jai.jar         OME JAI	0.1.3-SNAPSHOT	4 April 2024	94f975dfe39c34c8c39668ad0b0f54974375920e
Jar:        lib/server/ome-mdbtools.jar    MDB Tools (Java port)	5.3.3-SNAPSHOT	4 April 2024	94f975dfe39c34c8c39668ad0b0f54974375920e
Jar:        lib/server/ome-poi.jar         OME POI	5.3.9-SNAPSHOT	4 April 2024	94f975dfe39c34c8c39668ad0b0f54974375920e
Jar:        lib/server/ome-xml.jar         OME XML library	6.3.5-SNAPSHOT	4 April 2024	94f975dfe39c34c8c39668ad0b0f54974375920e
Jar:        lib/server/omero-blitz.jar     jar	5.7.3-SNAPSHOT		
Jar:        lib/server/omero-common.jar    jar	5.6.5-SNAPSHOT		
Jar:        lib/server/omero-gateway.jar   jar	5.9.1-SNAPSHOT		
Jar:        lib/server/omero-model.jar     jar	5.6.14-SNAPSHOT		
Jar:        lib/server/omero-renderer.jar  jar	5.5.16-SNAPSHOT		
Jar:        lib/server/omero-romio.jar     jar	5.7.6-SNAPSHOT		
Jar:        lib/server/omero-server.jar    jar	5.6.11-SNAPSHOT		
+ 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 '' ']'
+ '[' -n /bin/bash -o -n '' ']'
+ hash -r
+ '[' -n '' ']'
+ unset VIRTUAL_ENV
+ '[' '!' '' = nondestructive ']'
+ unset -f deactivate
Finished: SUCCESS