13:48:35 Started by user devspace
13:48:35 Running as SYSTEM
13:48:35 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
13:48:35 [OMERO-server] $ /bin/bash -xe /tmp/jenkins6822745944937635139.sh
13:48:35 + source /home/settings.env
13:48:35 ++ OMERO_DB_HOST=pg
13:48:35 ++ OMERO_DB_USER=postgres
13:48:35 ++ OMERO_DB_PASS=
13:48:35 ++ OMERO_ROOT_PASS=omero
13:48:35 ++ OMERO_DATA_DIR=/OMERO
13:48:35 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
13:48:35 + OMERO_DB_NAME=OMERO-server
13:48:35 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
13:48:35 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
13:48:35 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
13:48:35 + OMERO_DATA_DIR=/home/omero/omero-server-data
13:48:35 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
13:48:35 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
13:48:35 ++ deactivate nondestructive
13:48:35 ++ '[' -n '' ']'
13:48:35 ++ '[' -n '' ']'
13:48:35 ++ '[' -n /bin/bash -o -n '' ']'
13:48:35 ++ hash -r
13:48:35 ++ '[' -n '' ']'
13:48:35 ++ unset VIRTUAL_ENV
13:48:35 ++ '[' '!' nondestructive = nondestructive ']'
13:48:35 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
13:48:35 ++ export VIRTUAL_ENV
13:48:35 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
13:48:35 ++ 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
13:48:35 ++ export PATH
13:48:35 ++ '[' -n '' ']'
13:48:35 ++ '[' -z '' ']'
13:48:35 ++ _OLD_VIRTUAL_PS1=
13:48:35 ++ PS1='(.venv3) '
13:48:35 ++ export PS1
13:48:35 ++ '[' -n /bin/bash -o -n '' ']'
13:48:35 ++ hash -r
13:48:35 + omero admin stop
13:48:37 Server not running
13:48:37 + echo not running
13:48:37 not running
13:48:37 + sleep 5
13:48:42 + deactivate
13:48:42 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
13:48:42 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
13:48:42 + export PATH
13:48:42 + unset _OLD_VIRTUAL_PATH
13:48:42 + '[' -n '' ']'
13:48:42 + '[' -n /bin/bash -o -n '' ']'
13:48:42 + hash -r
13:48:42 + '[' -n '' ']'
13:48:42 + unset VIRTUAL_ENV
13:48:42 + '[' '!' '' = nondestructive ']'
13:48:42 + unset -f deactivate
13:48:42 + rm -rf /home/omero/workspace/OMERO-server/.venv3
13:48:42 + python3 -m venv /home/omero/workspace/OMERO-server/.venv3
13:48:45 + '[' false = true ']'
13:48:45 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
13:48:45 Skipping PURGE_DATA:CleanDbAndRepo
13:48:45 + rm -rf /home/omero/workspace/OMERO-server/a.fake /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-5.19.1.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
13:48:48 Copied 1 artifact from "OMERO-build" build number 7
13:48:48 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 7
13:48:48 Copied 2 artifacts from "OMERO-build-build" build number 7
13:48:48 [OMERO-server] $ /bin/bash -xe /tmp/jenkins9596272663132140216.sh
13:48:48 + source /home/settings.env
13:48:48 ++ OMERO_DB_HOST=pg
13:48:48 ++ OMERO_DB_USER=postgres
13:48:48 ++ OMERO_DB_PASS=
13:48:48 ++ OMERO_ROOT_PASS=omero
13:48:48 ++ OMERO_DATA_DIR=/OMERO
13:48:48 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
13:48:48 + OMERO_DB_NAME=OMERO-server
13:48:48 + OMERO_DATA_DIR=/home/omero/omero-server-data
13:48:48 + mkdir -p /home/omero/omero-server-data
13:48:48 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
13:48:48 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
13:48:48 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
13:48:48 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
13:48:48 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
13:48:48 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
13:48:48 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
13:48:48 ++ ls OMERO.server-5.6.3-437-854b934e23-ice36.zip
13:48:48 + ZIP=OMERO.server-5.6.3-437-854b934e23-ice36.zip
13:48:48 + '[' '!' -z '' ']'
13:48:48 + DIST=OMERO.server-5.6.3-437-854b934e23-ice36
13:48:48 + unzip OMERO.server-5.6.3-437-854b934e23-ice36.zip
13:48:48 Archive: OMERO.server-5.6.3-437-854b934e23-ice36.zip
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/blitz/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/grid/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/profiles/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/error/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/grid/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/luts/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/luts/janelia/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/luts/ncsa_paledit/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/luts/wcif/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/analysis_scripts/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/annotation_scripts/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/export_scripts/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/figure_scripts/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/import_scripts/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/util_scripts/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/server/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/share/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/share/licenses/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/misc/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__1/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__10/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__11/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__2/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__3/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__4/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__5/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__6/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__7/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__8/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__9/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3__4/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3__5/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3__6/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3__7/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO4.1__0/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO4.2__0/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO4.2__0/t/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO4.3__0/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO4.4__0/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO4__0/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.0__0/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.1__1/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.2__0/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4DEV__1/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4DEV__2/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4DEV__3/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/
13:48:48 creating: OMERO.server-5.6.3-437-854b934e23-ice36/var/
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/LICENSE.txt
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/backup.cfg
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/blitz/mail-senders.example
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/blitz/mail-server.example
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/build.properties
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/env.bat
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/env.sh
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/hibernate.properties
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/ice.config
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/logback-cli.xml
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/logback-indexing-cli.xml
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/logback-indexing.xml
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/logback.xml
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/mime.types
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/node1.cfg
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/node2.cfg
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/omero.properties
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/profiles/psql
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/rollover.cfg
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/Windows.cfg
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/error/maintainance.html
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/grid/README
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/grid/default.xml
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/grid/templates.xml
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/grid/windefault.xml
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/ice.config
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/internal.cfg
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/master.cfg
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/robot.template
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/testdropbox.config
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/history.rst
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/OMEZarrReader.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/activation.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/aggdesigner-algorithm.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/aircompressor.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/annotations.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/antlr.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/aopalliance.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/apache-client.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/arns.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/auth.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/avatica-core.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/avatica-metrics.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/aws-core.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/aws-query-protocol.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/aws-xml-protocol.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/base.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-all.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-anim.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-awt-util.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-bridge.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-codec.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-constants.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-css.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-dom.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-ext.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-extension.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-gui-util.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-gvt.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-i18n.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-parser.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-rasterizer-ext.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-rasterizer.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-script.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-slideshow.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-squiggle-ext.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-squiggle.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-svg-dom.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-svgbrowser.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-svggen.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-svgpp.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-svgrasterizer.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-swing.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-transcoder.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-ttf2svg.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-util.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-xml.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/btm.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/bufr.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/c3p0.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/calcite-core.jar
13:48:48 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/calcite-linq4j.jar
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13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/psql-footer.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/psql-header.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/schema.sql
13:48:51 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/views.sql
13:48:51 + rm -f OMERO.server-5.6.3-437-854b934e23-ice36.zip
13:48:51 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-437-854b934e23-ice36 /home/omero/workspace/OMERO-server/OMERO.server
13:48:51 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
13:48:51 ++ deactivate nondestructive
13:48:51 ++ '[' -n '' ']'
13:48:51 ++ '[' -n '' ']'
13:48:51 ++ '[' -n /bin/bash -o -n '' ']'
13:48:51 ++ hash -r
13:48:51 ++ '[' -n '' ']'
13:48:51 ++ unset VIRTUAL_ENV
13:48:51 ++ '[' '!' nondestructive = nondestructive ']'
13:48:51 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
13:48:51 ++ export VIRTUAL_ENV
13:48:51 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
13:48:51 ++ 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
13:48:51 ++ export PATH
13:48:51 ++ '[' -n '' ']'
13:48:51 ++ '[' -z '' ']'
13:48:51 ++ _OLD_VIRTUAL_PS1=
13:48:51 ++ PS1='(.venv3) '
13:48:51 ++ export PS1
13:48:51 ++ '[' -n /bin/bash -o -n '' ']'
13:48:51 ++ hash -r
13:48:51 + 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
13:48:51 Collecting zeroc-ice==3.6.5
13:48:52 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)
13:48:53 Installing collected packages: zeroc-ice
13:48:54 Successfully installed zeroc-ice-3.6.5
13:48:54 WARNING: You are using pip version 21.2.3; however, version 24.0 is available.
13:48:54 You should consider upgrading via the '/home/omero/workspace/OMERO-server/.venv3/bin/python3 -m pip install --upgrade pip' command.
13:48:54 + pip install -U pip future
13:48:54 Requirement already satisfied: pip in ./.venv3/lib/python3.9/site-packages (21.2.3)
13:48:55 Collecting pip
13:48:55 Using cached pip-24.0-py3-none-any.whl (2.1 MB)
13:48:55 Collecting future
13:48:55 Using cached future-1.0.0-py3-none-any.whl (491 kB)
13:48:55 Installing collected packages: pip, future
13:48:55 Attempting uninstall: pip
13:48:55 Found existing installation: pip 21.2.3
13:48:55 Uninstalling pip-21.2.3:
13:48:55 Successfully uninstalled pip-21.2.3
13:48:57 Successfully installed future-1.0.0 pip-24.0
13:48:57 + pip install markdown
13:48:57 Collecting markdown
13:48:57 Using cached Markdown-3.6-py3-none-any.whl.metadata (7.0 kB)
13:48:57 Collecting importlib-metadata>=4.4 (from markdown)
13:48:57 Using cached importlib_metadata-7.1.0-py3-none-any.whl.metadata (4.7 kB)
13:48:58 Collecting zipp>=0.5 (from importlib-metadata>=4.4->markdown)
13:48:58 Using cached zipp-3.18.1-py3-none-any.whl.metadata (3.5 kB)
13:48:58 Using cached Markdown-3.6-py3-none-any.whl (105 kB)
13:48:58 Using cached importlib_metadata-7.1.0-py3-none-any.whl (24 kB)
13:48:58 Using cached zipp-3.18.1-py3-none-any.whl (8.2 kB)
13:48:58 Installing collected packages: zipp, importlib-metadata, markdown
13:48:58 Successfully installed importlib-metadata-7.1.0 markdown-3.6 zipp-3.18.1
13:48:58 + pip install reportlab
13:48:58 Collecting reportlab
13:48:59 Using cached reportlab-4.1.0-py3-none-any.whl.metadata (1.4 kB)
13:48:59 Collecting pillow>=9.0.0 (from reportlab)
13:48:59 Using cached pillow-10.2.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.7 kB)
13:48:59 Collecting chardet (from reportlab)
13:48:59 Using cached chardet-5.2.0-py3-none-any.whl.metadata (3.4 kB)
13:48:59 Using cached reportlab-4.1.0-py3-none-any.whl (1.9 MB)
13:48:59 Using cached pillow-10.2.0-cp39-cp39-manylinux_2_28_x86_64.whl (4.5 MB)
13:48:59 Using cached chardet-5.2.0-py3-none-any.whl (199 kB)
13:48:59 Installing collected packages: pillow, chardet, reportlab
13:49:01 Successfully installed chardet-5.2.0 pillow-10.2.0 reportlab-4.1.0
13:49:01 + pip install omego
13:49:02 Collecting omego
13:49:02 Using cached omego-0.7.0-py3-none-any.whl
13:49:02 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omego) (1.0.0)
13:49:02 Collecting yaclifw>=0.1.1 (from omego)
13:49:02 Using cached yaclifw-0.2.0-py3-none-any.whl
13:49:02 Collecting six (from yaclifw>=0.1.1->omego)
13:49:02 Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
13:49:02 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
13:49:02 Installing collected packages: six, yaclifw, omego
13:49:02 Successfully installed omego-0.7.0 six-1.16.0 yaclifw-0.2.0
13:49:02 + pip install tables
13:49:03 Collecting tables
13:49:03 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
13:49:03 Collecting numpy>=1.19.0 (from tables)
13:49:03 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
13:49:03 Collecting numexpr>=2.6.2 (from tables)
13:49:03 Using cached numexpr-2.9.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.9 kB)
13:49:03 Collecting packaging (from tables)
13:49:03 Using cached packaging-24.0-py3-none-any.whl.metadata (3.2 kB)
13:49:03 Collecting py-cpuinfo (from tables)
13:49:03 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
13:49:03 Collecting blosc2>=2.3.0 (from tables)
13:49:03 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.2 kB)
13:49:03 Collecting ndindex>=1.4 (from blosc2>=2.3.0->tables)
13:49:03 Using cached ndindex-1.8-py3-none-any.whl.metadata (3.4 kB)
13:49:04 Collecting msgpack (from blosc2>=2.3.0->tables)
13:49:04 Using cached msgpack-1.0.8-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.1 kB)
13:49:04 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
13:49:04 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
13:49:04 Using cached numexpr-2.9.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (374 kB)
13:49:04 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
13:49:04 Using cached packaging-24.0-py3-none-any.whl (53 kB)
13:49:04 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
13:49:04 Using cached ndindex-1.8-py3-none-any.whl (91 kB)
13:49:04 Using cached msgpack-1.0.8-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (385 kB)
13:49:04 Installing collected packages: py-cpuinfo, packaging, numpy, ndindex, msgpack, numexpr, blosc2, tables
13:49:07 Successfully installed blosc2-2.5.1 msgpack-1.0.8 ndindex-1.8 numexpr-2.9.0 numpy-1.26.4 packaging-24.0 py-cpuinfo-9.0.0 tables-3.9.2
13:49:07 + pip install jinja2
13:49:08 Collecting jinja2
13:49:08 Using cached Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
13:49:08 Collecting MarkupSafe>=2.0 (from jinja2)
13:49:08 Using cached MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
13:49:08 Using cached Jinja2-3.1.3-py3-none-any.whl (133 kB)
13:49:08 Using cached MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
13:49:08 Installing collected packages: MarkupSafe, jinja2
13:49:08 Successfully installed MarkupSafe-2.1.5 jinja2-3.1.3
13:49:08 + pip install omero-py
13:49:08 Collecting omero-py
13:49:08 Using cached omero_py-5.19.0-py3-none-any.whl.metadata (6.6 kB)
13:49:09 Collecting urllib3<2 (from omero-py)
13:49:09 Using cached urllib3-1.26.18-py2.py3-none-any.whl.metadata (48 kB)
13:49:09 Collecting appdirs (from omero-py)
13:49:09 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
13:49:09 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py) (1.0.0)
13:49:09 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py) (1.26.4)
13:49:09 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py) (10.2.0)
13:49:09 Collecting PyYAML (from omero-py)
13:49:09 Using cached PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
13:49:09 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py) (3.6.5)
13:49:09 Collecting requests (from omero-py)
13:49:09 Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
13:49:09 Collecting portalocker (from omero-py)
13:49:09 Using cached portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB)
13:49:09 Collecting charset-normalizer<4,>=2 (from requests->omero-py)
13:49:09 Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
13:49:09 Collecting idna<4,>=2.5 (from requests->omero-py)
13:49:09 Using cached idna-3.6-py3-none-any.whl.metadata (9.9 kB)
13:49:09 Collecting certifi>=2017.4.17 (from requests->omero-py)
13:49:09 Using cached certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
13:49:09 Using cached omero_py-5.19.0-py3-none-any.whl (2.8 MB)
13:49:09 Using cached urllib3-1.26.18-py2.py3-none-any.whl (143 kB)
13:49:09 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
13:49:09 Using cached portalocker-2.8.2-py3-none-any.whl (17 kB)
13:49:09 Using cached PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB)
13:49:09 Using cached requests-2.31.0-py3-none-any.whl (62 kB)
13:49:09 Using cached certifi-2024.2.2-py3-none-any.whl (163 kB)
13:49:09 Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB)
13:49:09 Using cached idna-3.6-py3-none-any.whl (61 kB)
13:49:09 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, idna, charset-normalizer, certifi, requests, omero-py
13:49:12 Successfully installed PyYAML-6.0.1 appdirs-1.4.4 certifi-2024.2.2 charset-normalizer-3.3.2 idna-3.6 omero-py-5.19.0 portalocker-2.8.2 requests-2.31.0 urllib3-1.26.18
13:49:12 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
13:49:12 Collecting omero-metadata
13:49:12 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-c82w05zg/omero-metadata_29efaa95f6ec4c89992a0c2532a298c8
13:49:12 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-c82w05zg/omero-metadata_29efaa95f6ec4c89992a0c2532a298c8
13:49:13 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 1d3d76cb73401efbb04e5efafc7c7e04aa91a5bc
13:49:13 Installing build dependencies: started
13:49:15 Installing build dependencies: finished with status 'done'
13:49:15 Getting requirements to build wheel: started
13:49:15 Getting requirements to build wheel: finished with status 'done'
13:49:15 Installing backend dependencies: started
13:49:16 Installing backend dependencies: finished with status 'done'
13:49:16 Preparing metadata (pyproject.toml): started
13:49:16 Preparing metadata (pyproject.toml): finished with status 'done'
13:49:16 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (5.19.0)
13:49:16 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (6.0.1)
13:49:16 Requirement already satisfied: jinja2 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (3.1.3)
13:49:16 Collecting pandas (from omero-metadata)
13:49:16 Using cached pandas-2.2.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
13:49:16 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.18)
13:49:16 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
13:49:16 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
13:49:16 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.4)
13:49:16 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (10.2.0)
13:49:16 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)
13:49:16 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.31.0)
13:49:16 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.8.2)
13:49:16 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib/python3.9/site-packages (from jinja2->omero-metadata) (2.1.5)
13:49:17 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
13:49:17 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
13:49:17 Collecting pytz>=2020.1 (from pandas->omero-metadata)
13:49:17 Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
13:49:17 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
13:49:17 Using cached tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB)
13:49:17 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)
13:49:17 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)
13:49:17 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)
13:49:17 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)
13:49:17 Using cached pandas-2.2.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.0 MB)
13:49:17 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
13:49:17 Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB)
13:49:17 Using cached tzdata-2024.1-py2.py3-none-any.whl (345 kB)
13:49:17 Building wheels for collected packages: omero-metadata
13:49:17 Building wheel for omero-metadata (pyproject.toml): started
13:49:17 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
13:49:17 Created wheel for omero-metadata: filename=omero_metadata-0.12.1.dev0-py3-none-any.whl size=39111 sha256=a315f8a59c00cc54136bd50627e54c800d32a905182e81817c0f5407fdda8f0c
13:49:17 Stored in directory: /tmp/pip-ephem-wheel-cache-6o3owei6/wheels/64/09/47/3b86b706f8f6f4bec1b7fd6641d2e4a09814e754fa4c85c82d
13:49:17 Successfully built omero-metadata
13:49:17 Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
13:49:22 Successfully installed omero-metadata-0.12.1.dev0 pandas-2.2.1 python-dateutil-2.9.0.post0 pytz-2024.1 tzdata-2024.1
13:49:22 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
13:49:23 Collecting omero-cli-render
13:49:23 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-2_yx5xwu/omero-cli-render_78884e957b9c43b0b0017693e3ab8cfe
13:49:23 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-2_yx5xwu/omero-cli-render_78884e957b9c43b0b0017693e3ab8cfe
13:49:24 Running command git checkout -b merge_ci --track origin/merge_ci
13:49:24 Switched to a new branch 'merge_ci'
13:49:24 branch 'merge_ci' set up to track 'origin/merge_ci'.
13:49:24 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit c9d362b6f278aecfcdf112f038624c6b0dae202d
13:49:24 Installing build dependencies: started
13:49:26 Installing build dependencies: finished with status 'done'
13:49:26 Getting requirements to build wheel: started
13:49:26 Getting requirements to build wheel: finished with status 'done'
13:49:26 Installing backend dependencies: started
13:49:27 Installing backend dependencies: finished with status 'done'
13:49:27 Preparing metadata (pyproject.toml): started
13:49:27 Preparing metadata (pyproject.toml): finished with status 'done'
13:49:27 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (6.0.1)
13:49:27 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (5.19.0)
13:49:27 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (1.0.0)
13:49:27 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.18)
13:49:27 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
13:49:27 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.4)
13:49:27 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (10.2.0)
13:49:27 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)
13:49:27 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.31.0)
13:49:27 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.8.2)
13:49:27 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)
13:49:27 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)
13:49:27 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)
13:49:27 Building wheels for collected packages: omero-cli-render
13:49:27 Building wheel for omero-cli-render (pyproject.toml): started
13:49:28 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
13:49:28 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.1.dev0-py3-none-any.whl size=18018 sha256=bc01312f839abc44705871158a1c5fa4ae6150e71d8b359f19842c76a8ccde3b
13:49:28 Stored in directory: /tmp/pip-ephem-wheel-cache-0yraz1si/wheels/58/32/1b/746489b3c7c17a98c6cd7195bdd3b426dd4137caeb1045a994
13:49:28 Successfully built omero-cli-render
13:49:28 Installing collected packages: omero-cli-render
13:49:28 Successfully installed omero-cli-render-0.8.1.dev0
13:49:28 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
13:49:28 Collecting omero-cli-duplicate
13:49:28 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-zn8h6w3x/omero-cli-duplicate_62a851751c3a4ff99a2d3287b4202e07
13:49:28 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-zn8h6w3x/omero-cli-duplicate_62a851751c3a4ff99a2d3287b4202e07
13:49:29 Running command git checkout -b merge_ci --track origin/merge_ci
13:49:30 Switched to a new branch 'merge_ci'
13:49:30 branch 'merge_ci' set up to track 'origin/merge_ci'.
13:49:30 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 6a0c1d0cb6c23071709dfe245393cb37747601b9
13:49:30 Installing build dependencies: started
13:49:31 Installing build dependencies: finished with status 'done'
13:49:31 Getting requirements to build wheel: started
13:49:31 Getting requirements to build wheel: finished with status 'done'
13:49:31 Installing backend dependencies: started
13:49:32 Installing backend dependencies: finished with status 'done'
13:49:32 Preparing metadata (pyproject.toml): started
13:49:32 Preparing metadata (pyproject.toml): finished with status 'done'
13:49:32 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib/python3.9/site-packages (from omero-cli-duplicate) (5.19.0)
13:49:32 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.18)
13:49:32 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
13:49:32 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
13:49:32 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.4)
13:49:32 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (10.2.0)
13:49:32 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.1)
13:49:32 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)
13:49:32 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.31.0)
13:49:32 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.8.2)
13:49:33 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)
13:49:33 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)
13:49:33 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)
13:49:33 Building wheels for collected packages: omero-cli-duplicate
13:49:33 Building wheel for omero-cli-duplicate (pyproject.toml): started
13:49:33 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
13:49:33 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11443 sha256=8ac3116a6a2f5e4ccbc701de0420d4104e10946fd720ff31f3db2697d1908a81
13:49:33 Stored in directory: /tmp/pip-ephem-wheel-cache-pmmbjf8h/wheels/f1/55/ac/0cb8b093a4c417e5157143839711e7613efa64eaa21c29ef84
13:49:33 Successfully built omero-cli-duplicate
13:49:33 Installing collected packages: omero-cli-duplicate
13:49:33 Successfully installed omero-cli-duplicate-0.4.1.dev0
13:49:33 + pip install omero-certificates
13:49:34 Collecting omero-certificates
13:49:34 Using cached omero_certificates-0.3.2-py3-none-any.whl.metadata (3.7 kB)
13:49:34 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-certificates) (5.19.0)
13:49:34 Collecting distro==1.8.0 (from omero-certificates)
13:49:34 Using cached distro-1.8.0-py3-none-any.whl.metadata (6.9 kB)
13:49:34 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.18)
13:49:34 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
13:49:34 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
13:49:34 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.4)
13:49:34 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (10.2.0)
13:49:34 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.1)
13:49:34 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)
13:49:34 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.31.0)
13:49:34 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.8.2)
13:49:34 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)
13:49:34 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)
13:49:34 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)
13:49:34 Using cached omero_certificates-0.3.2-py3-none-any.whl (13 kB)
13:49:34 Using cached distro-1.8.0-py3-none-any.whl (20 kB)
13:49:34 Installing collected packages: distro, omero-certificates
13:49:34 Successfully installed distro-1.8.0 omero-certificates-0.3.2
13:49:34 + for x in *.tar.gz
13:49:34 + pip install -U omero-dropbox-5.6.3.dev0.tar.gz
13:49:34 Processing ./omero-dropbox-5.6.3.dev0.tar.gz
13:49:35 Installing build dependencies: started
13:49:36 Installing build dependencies: finished with status 'done'
13:49:36 Getting requirements to build wheel: started
13:49:36 Getting requirements to build wheel: finished with status 'done'
13:49:36 Installing backend dependencies: started
13:49:37 Installing backend dependencies: finished with status 'done'
13:49:37 Preparing metadata (pyproject.toml): started
13:49:37 Preparing metadata (pyproject.toml): finished with status 'done'
13:49:37 Requirement already satisfied: omero-py in ./.venv3/lib/python3.9/site-packages (from omero-dropbox==5.6.3.dev0) (5.19.0)
13:49:37 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (1.26.18)
13:49:37 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (1.4.4)
13:49:37 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (1.0.0)
13:49:37 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (1.26.4)
13:49:37 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (10.2.0)
13:49:37 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (6.0.1)
13:49:37 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)
13:49:37 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (2.31.0)
13:49:37 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (2.8.2)
13:49:37 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)
13:49:37 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)
13:49:37 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)
13:49:37 Building wheels for collected packages: omero-dropbox
13:49:37 Building wheel for omero-dropbox (pyproject.toml): started
13:49:38 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
13:49:38 Created wheel for omero-dropbox: filename=omero_dropbox-5.6.3.dev0-py3-none-any.whl size=49057 sha256=222ffa1e8019cf23e920d7c48af4d4f41eff444c3a7fdd5342de94b79b6c6c03
13:49:38 Stored in directory: /home/omero/.cache/pip/wheels/a5/63/29/4452e52704e5ad491f397a0013b20ebb9d413ceb110f8101d1
13:49:38 Successfully built omero-dropbox
13:49:38 Installing collected packages: omero-dropbox
13:49:38 Successfully installed omero-dropbox-5.6.3.dev0
13:49:38 + for x in *.tar.gz
13:49:38 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
13:49:38 Processing ./omero_marshal-0.9.1.dev0.tar.gz
13:49:38 Installing build dependencies: started
13:49:40 Installing build dependencies: finished with status 'done'
13:49:40 Getting requirements to build wheel: started
13:49:40 Getting requirements to build wheel: finished with status 'done'
13:49:40 Installing backend dependencies: started
13:49:41 Installing backend dependencies: finished with status 'done'
13:49:41 Preparing metadata (pyproject.toml): started
13:49:41 Preparing metadata (pyproject.toml): finished with status 'done'
13:49:41 Building wheels for collected packages: omero_marshal
13:49:41 Building wheel for omero_marshal (pyproject.toml): started
13:49:42 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
13:49:42 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88031 sha256=05d8321d0c0903dd6a826471d0501ed6180fcacc4f83537734b52ed7f437f5c9
13:49:42 Stored in directory: /home/omero/.cache/pip/wheels/8b/40/f1/dbed071eff57c96e0824ead2a420a7a1a080f7fbdfe0431d7f
13:49:42 Successfully built omero_marshal
13:49:42 Installing collected packages: omero_marshal
13:49:42 Successfully installed omero_marshal-0.9.1.dev0
13:49:42 + for x in *.tar.gz
13:49:42 + pip install -U omero-py-5.19.1.dev0.tar.gz
13:49:42 Processing ./omero-py-5.19.1.dev0.tar.gz
13:49:43 Installing build dependencies: started
13:49:44 Installing build dependencies: finished with status 'done'
13:49:44 Getting requirements to build wheel: started
13:49:45 Getting requirements to build wheel: finished with status 'done'
13:49:45 Installing backend dependencies: started
13:49:45 Installing backend dependencies: finished with status 'done'
13:49:45 Preparing metadata (pyproject.toml): started
13:49:46 Preparing metadata (pyproject.toml): finished with status 'done'
13:49:46 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (1.26.18)
13:49:46 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (1.4.4)
13:49:46 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (1.0.0)
13:49:46 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (1.26.4)
13:49:46 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (10.2.0)
13:49:46 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (6.0.1)
13:49:46 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (3.6.5)
13:49:46 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (2.31.0)
13:49:46 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (2.8.2)
13:49:46 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.1.dev0) (3.3.2)
13:49:46 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.1.dev0) (3.6)
13:49:46 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.1.dev0) (2024.2.2)
13:49:46 Building wheels for collected packages: omero-py
13:49:46 Building wheel for omero-py (pyproject.toml): started
13:49:47 Building wheel for omero-py (pyproject.toml): finished with status 'done'
13:49:47 Created wheel for omero-py: filename=omero_py-5.19.1.dev0-py3-none-any.whl size=2781680 sha256=0e26d8cc198669d0d3661825b7d7bf31fecedb75cec47f68ff68d2fa3c8d11ac
13:49:47 Stored in directory: /home/omero/.cache/pip/wheels/52/ce/ea/f5d1427ab67c2783e3f124f0ebf8311109c5ac331893a591ad
13:49:47 Successfully built omero-py
13:49:47 Installing collected packages: omero-py
13:49:47 Attempting uninstall: omero-py
13:49:47 Found existing installation: omero-py 5.19.0
13:49:47 Uninstalling omero-py-5.19.0:
13:49:48 Successfully uninstalled omero-py-5.19.0
13:49:49 Successfully installed omero-py-5.19.1.dev0
13:49:50 + for x in *.tar.gz
13:49:50 + pip install -U omero-scripts-5.8.1.dev0.tar.gz
13:49:50 Processing ./omero-scripts-5.8.1.dev0.tar.gz
13:49:50 Installing build dependencies: started
13:49:52 Installing build dependencies: finished with status 'done'
13:49:52 Getting requirements to build wheel: started
13:49:52 Getting requirements to build wheel: finished with status 'done'
13:49:52 Installing backend dependencies: started
13:49:53 Installing backend dependencies: finished with status 'done'
13:49:53 Preparing metadata (pyproject.toml): started
13:49:53 Preparing metadata (pyproject.toml): finished with status 'done'
13:49:53 Building wheels for collected packages: omero-scripts
13:49:53 Building wheel for omero-scripts (pyproject.toml): started
13:49:53 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
13:49:53 Created wheel for omero-scripts: filename=omero_scripts-5.8.1.dev0-py3-none-any.whl size=116570 sha256=326f4887a69ca7f932a0069e670a8e39f5e3be80d81c740ac99e2ba21279ba4b
13:49:53 Stored in directory: /home/omero/.cache/pip/wheels/ef/a0/80/e3393129cedc64a3ad2b8c2fa437d83a3d318cba65d425f5cf
13:49:53 Successfully built omero-scripts
13:49:53 Installing collected packages: omero-scripts
13:49:53 Successfully installed omero-scripts-5.8.1.dev0
13:49:54 + for x in *.tar.gz
13:49:54 + pip install -U omero-web-5.25.1.dev0.tar.gz
13:49:54 Processing ./omero-web-5.25.1.dev0.tar.gz
13:49:54 Installing build dependencies: started
13:49:56 Installing build dependencies: finished with status 'done'
13:49:56 Getting requirements to build wheel: started
13:49:56 Getting requirements to build wheel: finished with status 'done'
13:49:56 Installing backend dependencies: started
13:49:57 Installing backend dependencies: finished with status 'done'
13:49:57 Preparing metadata (pyproject.toml): started
13:49:57 Preparing metadata (pyproject.toml): finished with status 'done'
13:49:57 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (5.19.1.dev0)
13:49:57 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.25.1.dev0)
13:49:57 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl.metadata (17 kB)
13:49:58 Collecting Django<4.3,>=4.2.3 (from omero-web==5.25.1.dev0)
13:49:58 Using cached Django-4.2.11-py3-none-any.whl.metadata (4.2 kB)
13:49:58 Collecting django-pipeline==2.1.0 (from omero-web==5.25.1.dev0)
13:49:58 Using cached django_pipeline-2.1.0-py3-none-any.whl.metadata (12 kB)
13:49:58 Collecting django-cors-headers==3.7.0 (from omero-web==5.25.1.dev0)
13:49:58 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
13:49:58 Collecting django-csp (from omero-web==5.25.1.dev0)
13:49:58 Using cached django_csp-3.8-py3-none-any.whl.metadata (2.7 kB)
13:49:58 Collecting whitenoise>=5.3.0 (from omero-web==5.25.1.dev0)
13:49:58 Using cached whitenoise-6.6.0-py3-none-any.whl.metadata (3.7 kB)
13:49:58 Collecting gunicorn>=19.3 (from omero-web==5.25.1.dev0)
13:49:58 Using cached gunicorn-21.2.0-py3-none-any.whl.metadata (4.1 kB)
13:49:58 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)
13:49:58 Requirement already satisfied: Pillow in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (10.2.0)
13:49:58 Requirement already satisfied: pytz in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (2024.1)
13:49:58 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (2.8.2)
13:49:58 Requirement already satisfied: packaging in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (24.0)
13:49:59 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.25.1.dev0)
13:49:59 Using cached asgiref-3.8.0-py3-none-any.whl.metadata (9.3 kB)
13:49:59 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.25.1.dev0)
13:49:59 Using cached sqlparse-0.4.4-py3-none-any.whl.metadata (4.0 kB)
13:49:59 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)
13:49:59 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)
13:49:59 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)
13:49:59 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)
13:49:59 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)
13:49:59 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)
13:49:59 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)
13:49:59 Collecting typing-extensions>=4 (from asgiref<4,>=3.6.0->Django<4.3,>=4.2.3->omero-web==5.25.1.dev0)
13:49:59 Using cached typing_extensions-4.10.0-py3-none-any.whl.metadata (3.0 kB)
13:49:59 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)
13:49:59 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)
13:49:59 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)
13:49:59 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
13:49:59 Using cached django_pipeline-2.1.0-py3-none-any.whl (38 kB)
13:49:59 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl (25 kB)
13:49:59 Using cached Django-4.2.11-py3-none-any.whl (8.0 MB)
13:49:59 Using cached gunicorn-21.2.0-py3-none-any.whl (80 kB)
13:49:59 Using cached whitenoise-6.6.0-py3-none-any.whl (19 kB)
13:49:59 Using cached django_csp-3.8-py3-none-any.whl (17 kB)
13:49:59 Using cached asgiref-3.8.0-py3-none-any.whl (23 kB)
13:49:59 Using cached sqlparse-0.4.4-py3-none-any.whl (41 kB)
13:49:59 Using cached typing_extensions-4.10.0-py3-none-any.whl (33 kB)
13:49:59 Building wheels for collected packages: omero-web
13:49:59 Building wheel for omero-web (pyproject.toml): started
13:50:00 Building wheel for omero-web (pyproject.toml): finished with status 'done'
13:50:00 Created wheel for omero-web: filename=omero_web-5.25.1.dev0-py3-none-any.whl size=2769903 sha256=3ac7394579fb3a3557b3648943bef33b113233bcf5f1098f79fe63dfef7fc919
13:50:00 Stored in directory: /home/omero/.cache/pip/wheels/c5/4f/aa/011f4ecfdcda915571d213b068a736fbddf1b36b2e590de11a
13:50:00 Successfully built omero-web
13:50:01 Installing collected packages: django-pipeline, whitenoise, typing-extensions, sqlparse, gunicorn, concurrent-log-handler, asgiref, Django, django-csp, django-cors-headers, omero-web
13:50:04 Successfully installed Django-4.2.11 asgiref-3.8.0 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
13:50:04 + omero config set omero.db.name OMERO-server
13:50:05 + omero config set omero.db.host pg
13:50:06 + omero config set omero.db.user postgres
13:50:07 + omero config set omero.data.dir /home/omero/omero-server-data
13:50:09 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
13:50:10 + omero config set omero.db.poolsize 25
13:50:11 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
13:50:13 + omero config set omero.security.trustStorePassword changeit
13:50:14 + omero config set omero.mail.config true
13:50:15 + omero config set omero.mail.from qa@openmicroscopy.org.uk
13:50:16 + omero config set omero.mail.host smtp.dundee.ac.uk
13:50:18 + omero certificates
13:50:19 OpenSSL 3.0.7 1 Nov 2022 (Library: OpenSSL 3.0.7 1 Nov 2022)
13:50:19 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
13:50:19 + '[' false = true ']'
13:50:19 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
13:50:19 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
13:50:19 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
13:50:19 2024-03-21 13:50:19,785 [ omego.db] DEBUG dbcommand => upgrade
13:50:19 2024-03-21 13:50:19,785 [ omego.db] DEBUG dbhost => localhost
13:50:19 2024-03-21 13:50:19,785 [ omego.db] DEBUG dbname => OMERO-server
13:50:19 2024-03-21 13:50:19,785 [ omego.db] DEBUG dbpass => omero
13:50:19 2024-03-21 13:50:19,785 [ omego.db] DEBUG dbuser => omero
13:50:19 2024-03-21 13:50:19,785 [ omego.db] DEBUG rootpass => omero
13:50:19 2024-03-21 13:50:19,785 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
13:50:19 2024-03-21 13:50:19,785 [omego.extern] INFO Executing : omero version
13:50:20 OMERO.py version:
13:50:21 OMERO.server version:
13:50:21 5.6.3-437-854b934e23-ice36
13:50:21 5.19.1.dev0
13:50:21 2024-03-21 13:50:21,192 [omego.extern] INFO Completed [1.407 s]
13:50:21 2024-03-21 13:50:21,192 [omego.extern] DEBUG Using omero CLI from omero
13:50:21 2024-03-21 13:50:21,192 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
13:50:21 2024-03-21 13:50:21,192 [omego.extern] INFO Running [current environment]: omero config get --show-password
13:50:21 2024-03-21 13:50:21,192 [omego.extern] INFO Executing : omero config get --show-password
13:50:22 2024-03-21 13:50:22,537 [omego.extern] INFO Completed [1.345 s]
13:50:22 2024-03-21 13:50:22,538 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
13:50:22 2024-03-21 13:50:22,538 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
13:50:22 2024-03-21 13:50:22,544 [omego.extern] INFO Completed [0.006 s]
13:50:22 2024-03-21 13:50:22,544 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.2\n'
13:50:22 2024-03-21 13:50:22,544 [ omego.db] INFO psql version: psql (PostgreSQL) 16.2
13:50:22
13:50:22 2024-03-21 13:50:22,544 [omego.extern] INFO Running [current environment]: omero config get --show-password
13:50:22 2024-03-21 13:50:22,544 [omego.extern] INFO Executing : omero config get --show-password
13:50:23 2024-03-21 13:50:23,850 [omego.extern] INFO Completed [1.306 s]
13:50:23 2024-03-21 13:50:23,851 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
13:50:23 2024-03-21 13:50:23,851 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
13:50:24 2024-03-21 13:50:24,010 [omego.extern] INFO Completed [0.159 s]
13:50:24 2024-03-21 13:50:24,010 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.4") at port "5432".\n'
13:50:24 2024-03-21 13:50:24,010 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
13:50:24 2024-03-21 13:50:24,010 [omego.extern] INFO Running [current environment]: omero config get --show-password
13:50:24 2024-03-21 13:50:24,010 [omego.extern] INFO Executing : omero config get --show-password
13:50:25 2024-03-21 13:50:25,273 [omego.extern] INFO Completed [1.263 s]
13:50:25 2024-03-21 13:50:25,273 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
13:50:25 2024-03-21 13:50:25,273 [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
13:50:25 2024-03-21 13:50:25,423 [omego.extern] INFO Completed [0.150 s]
13:50:25 2024-03-21 13:50:25,423 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
13:50:25 2024-03-21 13:50:25,423 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
13:50:25 2024-03-21 13:50:25,425 [ omego.db] INFO Database is already at OMERO5.4__0
13:50:25 + export LANG=en_US.UTF-8
13:50:25 + LANG=en_US.UTF-8
13:50:25 + export LANGUAGE=en_US:en
13:50:25 + LANGUAGE=en_US:en
13:50:25 + export LC_ALL=en_US.UTF-8
13:50:25 + LC_ALL=en_US.UTF-8
13:50:25 + BUILD_ID=DONT_KILL_ME
13:50:25 + omero admin start
13:50:34 WARNING: lock files in /home/omero/omero-server-data
13:50:34 ----------------------------------------
13:50:34 /home/omero/omero-server-data/.omero/repository/7097ab62-1c9f-4ba2-a5e5-d5b1f868081e/.lock
13:50:34 ----------------------------------------
13:50:34
13:50:34 You may want to stop all server processes and remove
13:50:34 these files manually. Lock files can remain after an
13:50:34 abrupt server outage and are especially frequent on
13:50:34 remotely mounted filesystems like NFS.
13:50:34
13:50:34 No descriptor given. Using etc/grid/default.xml
13:50:42 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
13:50:42 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
13:50:42 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
13:50:42 Waiting on startup. Use CTRL-C to exit
13:50:42 + omero admin waitup
13:50:44 Waiting on startup. Use CTRL-C to exit
13:50:44 + omero admin diagnostics
13:50:45
13:50:45 ================================================================================
13:50:45 OMERO Diagnostics (admin)
13:50:45 ================================================================================
13:50:45
13:50:45 Commands: java -version 11.0.22 (/usr/bin/java)
13:50:45 Commands: python -V 3.9.18 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
13:50:45 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
13:50:45 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
13:50:45 Commands: psql --version 16.2 (/usr/bin/psql)
13:50:45 Commands: openssl version 3.0.71 (/usr/bin/openssl)
13:50:45
13:50:45 Component: OMERO.py 5.19.1.dev0
13:50:45 Component: OMERO.server 5.6.3-437-854b934e23-ice36
13:50:45
13:50:45 Server: icegridnode running
13:50:45 Server: Blitz-0 active (pid = 2325, enabled)
13:50:45 Server: DropBox activating (enabled)
13:50:45 Server: FileServer active (pid = 2388, enabled)
13:50:45 Server: Indexer-0 activating (enabled)
13:50:45 Server: MonitorServer active (pid = 2360, enabled)
13:50:45 Server: OMERO.Glacier2 active (pid = 2372, enabled)
13:50:45 Server: OMERO.IceStorm active (pid = 2391, enabled)
13:50:45 Server: PixelData-0 activating (enabled)
13:50:45 Server: Processor-0 activating (enabled)
13:50:45 Server: Tables-0 activating (enabled)
13:50:45 Server: TestDropBox inactive (enabled)
13:50:45
13:50:45 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
13:50:45 Log files: Blitz-0.log 21.9 KB errors=0 warnings=1
13:50:45 Log files: DropBox.log 121 B
13:50:45 Log files: FileServer.log 114 B
13:50:45 Log files: Indexer-0.log 114 B
13:50:45 Log files: MonitorServer.log 117 B
13:50:45 Log files: PixelData-0.log 114 B
13:50:45 Log files: Processor-0.log 281 B
13:50:45 Log files: Tables-0.log 281 B
13:50:45 Log files: TestDropBox.log n/a
13:50:45 Log files: master.err 869 B
13:50:45 Log files: master.out 41.5 KB
13:50:45 Log files: Total size 0.07 MB
13:50:45
13:50:45
13:50:45 Environment:OMERO_HOME=(unset)
13:50:45 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
13:50:45 Environment:OMERO_NODE=(unset)
13:50:45 Environment:OMERO_MASTER=(unset)
13:50:45 Environment:OMERO_USERDIR=(unset)
13:50:45 Environment:OMERO_TMPDIR=(unset)
13:50:45 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
13:50:45 Environment:PYTHONPATH=(unset)
13:50:45 Environment:ICE_HOME=/opt/ice-3.6.5
13:50:45 Environment:LD_LIBRARY_PATH=(unset)
13:50:45 Environment:DYLD_LIBRARY_PATH=(unset)
13:50:45
13:50:45 OMERO SSL port:4064
13:50:45 OMERO TCP port:4063
13:50:45 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
13:50:45 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
13:50:45
13:50:45 JVM settings: Blitz-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
13:50:45 JVM settings: Indexer-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
13:50:45 JVM settings: PixelData-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
13:50:45 JVM settings: Repository-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
13:50:45
13:50:45 Jar: lib/server/formats-api.jar Bio-Formats API 8.0.0-SNAPSHOT 21 March 2024 5c6c3e1ca3aac5f8e55dd5c5693604d128be5965
13:50:45 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.0.0-SNAPSHOT 21 March 2024 5c6c3e1ca3aac5f8e55dd5c5693604d128be5965
13:50:45 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.0.0-SNAPSHOT 21 March 2024 5c6c3e1ca3aac5f8e55dd5c5693604d128be5965
13:50:45 Jar: lib/server/ome-codecs.jar OME Codecs 1.0.1 8 December 2023 4f6bf7551ed2d1dfe8e74c857f6a694da40d1d97
13:50:45 Jar: lib/server/ome-common.jar OME Common Java 6.0.21 7 December 2023 fdace3279d4f6b682c5ba47ae4c49daac687459b
13:50:45 Jar: lib/server/ome-jai.jar OME JAI 0.1.3 3 August 2018 489959cb7d24c279249bc08181aa9f734158ca4e
13:50:45 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.2 7 August 2018 68ffca2a95750cbb96f0d11785851aa4a554c0a4
13:50:45 Jar: lib/server/ome-poi.jar OME POI 5.3.7 5 July 2022 79a44040fa896a7c78b4e25da6ba7f4dda204c8e
13:50:45 Jar: lib/server/ome-xml.jar OME XML library 6.3.4 7 December 2023 b4c6f4490d762138453225e0499346a6334f00e5
13:50:45 Jar: lib/server/omero-blitz.jar jar 5.7.3-SNAPSHOT
13:50:45 Jar: lib/server/omero-common.jar jar 5.6.5-SNAPSHOT
13:50:45 Jar: lib/server/omero-gateway.jar jar 5.9.1-SNAPSHOT
13:50:45 Jar: lib/server/omero-model.jar jar 5.6.14-SNAPSHOT
13:50:45 Jar: lib/server/omero-renderer.jar jar 5.5.16-SNAPSHOT
13:50:45 Jar: lib/server/omero-romio.jar jar 5.7.6-SNAPSHOT
13:50:45 Jar: lib/server/omero-server.jar jar 5.6.11-SNAPSHOT
13:50:46 + deactivate
13:50:46 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
13:50:46 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
13:50:46 + export PATH
13:50:46 + unset _OLD_VIRTUAL_PATH
13:50:46 + '[' -n '' ']'
13:50:46 + '[' -n /bin/bash -o -n '' ']'
13:50:46 + hash -r
13:50:46 + '[' -n '' ']'
13:50:46 + unset VIRTUAL_ENV
13:50:46 + '[' '!' '' = nondestructive ']'
13:50:46 + unset -f deactivate
13:50:46 Finished: SUCCESS
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