added install of ij-opencv-plugins in fiji, as lipase uses them
the test of lipase can't currently succeed (it actually fails but the error is not currently detected) because lipase requires opencv.
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e8f23bb445
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3f534229fd
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@ -5,6 +5,7 @@ pipeline {
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steps {
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echo 'Initial setup...'
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sh './scripts/install_fiji.bash'
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sh 'export FIJI_ROOT_PATH=$(pwd); ./scripts/install_lipase_in_fiji.bash'
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// echo 'Create or update the virtual Python environment'
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// sh '/bin/bash ./src/CI/CI.bash -i ci_venv'
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}
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@ -1,5 +1,38 @@
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#!/bin/bash
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FIJI_ROOT_PATH='/Applications/Fiji.app'
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if [ $FIJI_ROOT_PATH = '' ]
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then
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echo "please define the location of Fiji via the FIJI_ROOT_PATH environment variable"
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return 1
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fi
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# function get_fiji_root_path()
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# {
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# if [ $FIJI_ROOT_PATH != '' ]
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# then
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# echo $FIJI_ROOT_PATH
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# return
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# fi
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# local fiji_root_path=''
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# case $(hostname) in
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# 'pr079234.spm.univ-rennes1.fr') # simpa-macbook2
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# fiji_root_path='/Applications/Fiji.app'
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# ;;
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# 'pr079180.spm.univ-rennes1.fr') # graffy-ws2
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# fiji_root_path='~/soft/Fiji.app'
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# ;;
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# *)
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# case $(whoami) in
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# 'jenkins-agent')
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# fiji_root_path="$(pwd)"
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# ;;
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# esac
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# ;;
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# esac
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# echo "$fiji_root_path"
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# }
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@ -200,9 +233,58 @@ function create_test_jar()
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accept_maven_scijava_org_certificate
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mvn -Dimagej.app.directory=/Applications/Fiji.app
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# on ubuntu :
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# [WARNING] Rule 2: org.apache.maven.plugins.enforcer.RequireJavaVersion failed with message:
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# Detected JDK Version: 11.0.4 is not in the allowed range [1.8.0-101,1.8.9999].
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# [INFO] ------------------------------------------------------------------------
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# [INFO] BUILD FAILURE
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# [INFO] ------------------------------------------------------------------------
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# [INFO] Total time: 06:03 min
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# [INFO] Finished at: 2019-09-23T16:57:17+02:00
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# [INFO] ------------------------------------------------------------------------
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# [ERROR] Failed to execute goal org.apache.maven.plugins:maven-enforcer-plugin:1.4.1:enforce (enforce-rules) on project example-script-collection: Some Enforcer rules have failed. Look above for specific messages explaining why the rule failed. -> [Help 1]
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popd
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}
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function ensure_ij_opencv_plugin_is_installed()
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{
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# enable IJ-OpenCV-plugins site because it's disabled by default
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# graffy@graffy-ws2:~$ zcat /home/graffy/soft/Fiji.app/db.xml.gz | grep IJ-Op | grep -v "jar" | grep -v "<plu"
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# <disabled-update-site name="IJ-OpenCV-plugins" url="https://sites.imagej.net/IJ-OpenCV/" official="true" description="Collection of plugins created using the IJ-OpenCV library -- a library that allows the connection of ImageJ and OpenCV." timestamp="20190819101544"/>
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# graffy@graffy-ws2:~$ history | less
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# graffy@graffy-ws2:~$ ~/soft/Fiji.app/ImageJ-linux64 --update edit-update-site IJ-OpenCV-plugins https://sites.imagej.net/IJ-OpenCV/
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# Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
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# Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
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# Done: Checksummer
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# graffy@graffy-ws2:~$ zcat /home/graffy/soft/Fiji.app/db.xml.gz | grep IJ-Op | grep -v "jar" | grep -v "<plu"
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# <update-site name="IJ-OpenCV-plugins" url="https://sites.imagej.net/IJ-OpenCV/" official="true" description="Collection of plugins created using the IJ-OpenCV library -- a library that allows the connection of ImageJ and OpenCV." timestamp="20190819101544"/>
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$FIJI_ROOT_PATH/ImageJ-linux64 --update edit-update-site IJ-OpenCV-plugins https://sites.imagej.net/IJ-OpenCV/
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# then apply an update to download and install IJ-OpenCV-plugins :
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# jars/IJ-OpenCV.jar
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# jars/javacv.far
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# jars/opencv-linux-x86.jar
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# jars/opencv-linux-x86_64.jar
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# jars/opencv-macosx-x86_64.jar
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# jars/opencv-windows-x86.jar
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# jars/opencv-windows-x86_64.jar
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# jars/opencv.jar
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# lib/haarcascade_frontalface_alt.xml
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# graffy@graffy-ws2:~$ ~/soft/Fiji.app/ImageJ-linux64 --update update
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# Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
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# Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
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# Done: Checksummer
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# Done: Downloading...
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# Done: Downloading...
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$FIJI_ROOT_PATH/ImageJ-linux64 --update update
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}
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function install_lipase_libs_in_fiji()
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{
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# https://imagej.net/Jython_Scripting
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@ -217,6 +299,9 @@ function install_lipase_libs_in_fiji()
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function install_lipase_in_fiji()
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{
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# lipase plugins require IJ-OpenCV-plugins
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ensure_ij_opencv_plugin_is_installed
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install_lipase_libs_in_fiji
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mkdir -p $FIJI_ROOT_PATH/plugins/Ipr
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