graffy
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lipase
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lipase is now released as a package on an owncloud directory 

This will ease the deployment to users.
This commit is contained in:
Guillaume Raffy 2019-10-04 18:48:35 +02:00
parent 61f6d9aeba
commit 8c3a5b0d72
4 changed files with 53 additions and 18 deletions
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22
Jenkinsfile vendored
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@ -1,5 +1,10 @@
pipeline { pipeline {
agent {label 'physix_agent'} agent {label 'physix_agent'}
environment {
// GRAFFY_OWNCLOUD_JENKINS_PWD's value has been obtained from https://cloud.ipr.univ-rennes1.fr as an app password and is defined in gitlab as a CI secret variable,
// then this app password has been declared to jenkins's credentials as a secret text with the name graffy-cloudipr-for-jenkinsipr
GRAFFY_OWNCLOUD_JENKINS_PWD = credentials('graffy-cloudipr-for-jenkinsipr')
}
stages { stages {
stage('Initial setup...') { stage('Initial setup...') {
steps { steps {
@ -21,13 +26,16 @@ pipeline {
// // sh '/bin/bash ./src/CI/CI.bash -d ci_venv' // // sh '/bin/bash ./src/CI/CI.bash -d ci_venv'
// } // }
// } // }
// stage('Releasing package...') { stage('Releasing package...') {
// steps { steps {
// echo 'Releasing package...' echo 'Releasing package...'
// // sh 'rm -rf $HOME/www/*' sh './scripts/release_lipase_package.bash'
// // sh 'cp -a ./src/doc/build/html/* $HOME/www/' //sh 'python -c "import owncloud; oc = owncloud.Client(''https://cloud.ipr.univ-rennes1.fr''); oc.login(''graffy'',''$OWNCLOUD_GITLABUR1_PWD''); oc.put_file(''downloads/%installer_file_name%', r'%installer_file_path%')"'
// } // sh 'make FIJI_ROOT_PATH=$(pwd)/Fiji.app package'
// } // sh 'rm -rf $HOME/www/*'
// sh 'cp -a ./src/doc/build/html/* $HOME/www/'
}
}
stage('Cleaning up...') { stage('Cleaning up...') {
steps { steps {
echo 'Cleaning artifacts...' echo 'Cleaning artifacts...'

32
Makefile
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@ -4,15 +4,19 @@ FIJI_EXE_PATH=$(FIJI_ROOT_PATH)/ImageJ-linux64
# RAW_IMAGES_ROOT_PATH:='/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images' # RAW_IMAGES_ROOT_PATH:='/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images'
RAW_IMAGES_ROOT_PATH:=$(shell echo ~/work/lipase/raw-images) RAW_IMAGES_ROOT_PATH:=$(shell echo ~/work/lipase/raw-images)
LIB_SRC_FILES=$(shell find ./src/lipase -name "*.py") LIB_SRC_FILES=$(shell find ./src/lipase -name "*.py")
LIPASE_VERSION=1.00
BUILD_ROOT_PATH=$(shell pwd)/build
PACKAGE_FILE_PATH=$(shell pwd)/lipase-$(LIPASE_VERSION).zip
.PHONY: all .PHONY: all
all: test0001 all: test
$(FIJI_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ip.lipase.lib.jar: $(LIB_SRC_FILES) $(BUILD_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar: $(LIB_SRC_FILES)
pushd ./src; \ pushd ./src; \
mkdir -p $(FIJI_ROOT_PATH)/jars/Lib ; \ mkdir -p $(BUILD_ROOT_PATH)/jars/Lib ; \
find ./lipase -name "*.py" > /tmp/files.txt ; \ find ./lipase -name "*.py" > /tmp/files.txt ; \
jar cvf $(FIJI_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ip.lipase.lib.jar @/tmp/files.txt ; \ jar cvf $(BUILD_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar @/tmp/files.txt ; \
popd popd
.PHONY: install_ij_opencv .PHONY: install_ij_opencv
@ -56,16 +60,17 @@ install_ij_opencv:
$(FIJI_ROOT_PATH)/ImageJ-linux64 --update update; \ $(FIJI_ROOT_PATH)/ImageJ-linux64 --update update; \
fi fi
.PHONY: install_lipase_libs $(PACKAGE_FILE_PATH): $(BUILD_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar
install_lipase_libs: $(FIJI_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ip.lipase.lib.jar install_ij_opencv mkdir -p $(BUILD_ROOT_PATH)/plugins/Ipr ; \
rsync -a ./src/ij-plugins/Ipr/ $(BUILD_ROOT_PATH)/plugins/Ipr/ ; \
zip -r $(PACKAGE_FILE_PATH) $(BUILD_ROOT_PATH)
.PHONY: install_lipase_plugins .PHONY: package
install_lipase_plugins: package: $(PACKAGE_FILE_PATH)
mkdir -p $(FIJI_ROOT_PATH)/plugins/Ipr ; \
rsync -a ./src/ij-plugins/Ipr/ $(FIJI_ROOT_PATH)/plugins/Ipr/
.PHONY: install .PHONY: install
install: install_lipase_libs install_lipase_plugins install: $(PACKAGE_FILE_PATH) install_ij_opencv
pushd $(FIJI_ROOT_PATH); unzip $(PACKAGE_FILE_PATH); popd
.PHONY: test0001 .PHONY: test0001
test0001: install test0001: install
@ -81,3 +86,8 @@ test0001: install
.PHONY: test .PHONY: test
test: test0001 test: test0001
.PHONY: clean
clean:
rm -Rf $(BUILD_ROOT_PATH)
rm -Rf $(PACKAGE_FILE_PATH)

2
scripts/cleanup.bash
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@ -1,2 +1,4 @@
#!/bin/bash #!/bin/bash
make clean
rm -Rf './Fiji.app' rm -Rf './Fiji.app'
rm -Rf './python.virtualenv'

15
scripts/release_lipase_package.bash Executable file
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@ -0,0 +1,15 @@
#!/bin/bash
LIPASE_PACKAGE_FILE_PATH=$(ls lipase*.zip)
echo "LIPASE_PACKAGE_FILE_PATH=$LIPASE_PACKAGE_FILE_PATH"
if [ "$GRAFFY_OWNCLOUD_JENKINS_PWD" = '' ]
then
echo "the value of the environment variable GRAFFY_OWNCLOUD_JENKINS_PWD is empty, while its contents are expected to come from JenkinsFile (this script is designed to be called from the accompanying JenkinsFile)"
exit 1
fi
virtualenv ./python.virtualenv
source ./python.virtualenv/bin/activate
pip install pyocclient # installs python owncloud module
python -c "import owncloud; oc = owncloud.Client('https://cloud.ipr.univ-rennes1.fr'); oc.login('graffy','$GRAFFY_OWNCLOUD_JENKINS_PWD'); oc.put_file('downloads/$LIPASE_PACKAGE_FILE_PATH', r'$LIPASE_PACKAGE_FILE_PATH')"