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Merged
adamjohnwright merged 6 commits into from
Nov 5, 2025
Merged

Update Jenkinsfile #22

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2ab5fae
Update Jenkinsfile
Jul 16, 2025
ef603d5
Fix indentation and formatting in Jenkinsfile
adamjohnwright Nov 5, 2025
fa794fa
Fix indentation in Jenkinsfile for docker run command
adamjohnwright Nov 5, 2025
3b350df
Escape password variable in Jenkinsfile
adamjohnwright Nov 5, 2025
1a077fb
Update Jenkinsfile
adamjohnwright Nov 5, 2025
c33b564
Refactor Docker commands in Jenkinsfile
adamjohnwright Nov 5, 2025
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134 changes: 91 additions & 43 deletions Jenkinsfile
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,15 @@ def utils = new Utilities()

pipeline {
agent any


environment {
ECR_URL_ANALYSIS_CORE = 'public.ecr.aws/reactome/analysis-core'
CONT_NAME_ANALYSIS_CORE = 'analysis_core_container'
ECR_URL_BIOMODELS_MAPPER = 'public.ecr.aws/reactome/biomodels-mapper'
CONT_NAME_BIOMODELS_MAPPER = 'biomodels_mapper_container'
ECR_URL_RELEASE_BIOMODELS = 'public.ecr.aws/reactome/release-biomodels'
CONT_NAME_RELEASE_BIOMODELS = 'release_biomodels_container'
}
stages {
// This stage checks that two upstream projects, OrthoinferenceStableIdentifierHistory and AddLinks-Insertion, were run successfully for their last build.
stage('Check OrthoinferenceStableIdentifierHistory and AddLinks-Insertion builds succeeded'){
Expand All @@ -18,7 +26,16 @@ pipeline {
}
}
}

stage('Setup: Pull and clean docker environment analysis core'){
steps{
sh "docker pull ${ECR_URL_ANALYSIS_CORE}:latest"
sh """
if docker ps -a --format '{{.Names}}' | grep -Eq '${CONT_NAME_ANALYSIS_CORE}'; then
docker rm -f ${CONT_NAME_ANALYSIS_CORE}
fi
"""
}
}
// Generates an intermediate analysis.bin file that is used by the biomodels-mapper.
stage('Setup: Generate BioModels analysis.bin file'){
steps{
Expand All @@ -29,36 +46,42 @@ pipeline {
// Builds analysis-core jar file and runs program that builds the analysis-biomodels-vXX.bin file.
dir("analysis-core"){
def analysisBinName = "analysis_v${releaseVersion}.bin"

// Builds jar file for analysis-core.
utils.buildJarFileWithPackage()

withCredentials([usernamePassword(credentialsId: 'neo4jUsernamePassword', passwordVariable: 'pass', usernameVariable: 'user')]){
sh "java -jar target/analysis-core-exec.jar --user $user --password $pass --output ./${analysisBinName} --verbose"
sh "mkdir -p output && rm -rf output/*"
sh """
CMD="docker run \\
-v \$(pwd)/output:/output \\
--net=host \\
--name ${CONT_NAME_ANALYSIS_CORE} ${ECR_URL_ANALYSIS_CORE}:latest \\
/bin/bash -c \\"java -jar target/analysis-core-exec.jar --user $user --password '\$pass' --output /output/${analysisBinName} --verbose\\""
eval "\$CMD"
"""
}

// Symlinks the analysis-biomodels-vXX.bin file to the generic analysis.bin path.
sh "cp ${analysisBinName} ${env.ANALYSIS_SERVICE_INPUT_ABS_PATH}/"
sh "sudo chown www-data:reactome ./output/${analysisBinName}"
sh "cp ./output/${analysisBinName} ${env.ANALYSIS_SERVICE_INPUT_ABS_PATH}/"
sh "ln -sf ${env.ANALYSIS_SERVICE_INPUT_ABS_PATH}/${analysisBinName} ${env.ANALYSIS_SERVICE_INPUT_ABS_PATH}/analysis.bin"

// Restart tomcat so that updated graph DB and analysis bin is being used.
// Restart Tomcat so that the updated graph DB and analysis bin are being used.
sh "sudo service tomcat9 stop"
sh "sudo service tomcat9 start"
}
}
}
}

stage("Build BioModels mapper"){
steps{
script{
utils.cloneOrUpdateLocalRepo("biomodels-mapper")
dir("biomodels-mapper"){
utils.buildJarFileWithPackage()
}
}
}
}
stage('Setup: Pull and clean docker environment biomodels mapper'){
steps{
sh "docker pull ${ECR_URL_BIOMODELS_MAPPER}:latest"
sh """
if docker ps -a --format '{{.Names}}' | grep -Eq '${CONT_NAME_BIOMODELS_MAPPER}'; then
docker rm -f ${CONT_NAME_BIOMODELS_MAPPER}
fi
"""
}
}

stage("Run BioModels mapper"){
steps{
Expand All @@ -67,31 +90,57 @@ pipeline {
dir("biomodels-mapper"){
sh "mkdir -p output"
sh "rm output/* -f"
sh "java -jar -Xms5120M -Xmx10240M target/biomodels-mapper-2.0.jar -o ./output/ -r /usr/local/reactomes/Reactome/production/AnalysisService/input/analysis.bin -b /tmp/BioModels_Database-r31_pub-sbml_files"
sh "rm -rf /tmp/BioModels_Database-r31_pub-sbml_files"
sh "mkdir -p input"
sh "rm input/* -f"
sh "cp /usr/local/reactomes/Reactome/production/AnalysisService/input/analysis.bin input/"
sh """
docker run \\
-v \$(pwd)/output:/output \\
-v \$(pwd)/input:/input \\
-v \$(pwd)/logs:/opt/biomodels-mapper/logs \\
--net=host --name ${CONT_NAME_BIOMODELS_MAPPER} ${ECR_URL_BIOMODELS_MAPPER}:latest \\
/bin/bash -c "java -jar -Xms5120M -Xmx10240M target/biomodels-mapper-2.0.jar -o /output/ -r /input/analysis.bin -b /tmp/BioModels_Database-r31_pub-sbml_files"
"""
sh "sudo chown www-data:reactome -R logs"
sh "sudo chown www-data:reactome output/models2pathways.tsv"
sh "sudo cp output/models2pathways.tsv ${env.ABS_DOWNLOAD_PATH}/${releaseVersion}/"
}
}
}
}

// Builds jar file for the release-biomodels project.
stage('Setup: Build release-biomodels jar file'){
steps{
script{
// BioModels Jar file
utils.buildJarFile()
}
}
}
stage('Setup: Pull and clean docker environment biomodels'){
steps{
sh "docker pull ${ECR_URL_RELEASE_BIOMODELS}:latest"
sh """
if docker ps -a --format '{{.Names}}' | grep -Eq '${CONT_NAME_RELEASE_BIOMODELS}'; then
docker rm -f ${CONT_NAME_RELEASE_BIOMODELS}
fi
"""
}
}

// Runs the release-biomodels program that adds the BioModels cross-references to the release_current DB.
stage('Main: Add BioModels links'){
steps{
script{
def releaseVersion = utils.getReleaseVersion()
withCredentials([file(credentialsId: 'Config', variable: 'ConfigFile')]) {
sh "java -jar target/biomodels-*-jar-with-dependencies.jar $ConfigFile ${env.ABS_DOWNLOAD_PATH}/${releaseVersion}/models2pathways.tsv"
sh "mkdir -p input"
sh "rm input/* -f"
sh "cp ${env.ABS_DOWNLOAD_PATH}/${releaseVersion}/models2pathways.tsv input"

sh "mkdir -p configs"
sh "rm -rf configs/*"
sh "cp $ConfigFile configs/config.prop"
sh """
docker run \\
-v \$(pwd)/input:/input \\
-v \$(pwd)/configs:/configs \\
--net=host --name ${CONT_NAME_RELEASE_BIOMODELS} ${ECR_URL_RELEASE_BIOMODELS}:latest \\
/bin/bash -c "java -jar target/biomodels-*-jar-with-dependencies.jar /configs/config.prop ./input/models2pathways.tsv"
"""
sh "rm configs/config.prop"
}
}
}
Expand All @@ -101,9 +150,14 @@ pipeline {
stage('Post: Back up DB'){
steps{
script{
withCredentials([usernamePassword(credentialsId: 'mySQLUsernamePassword', passwordVariable: 'pass', usernameVariable: 'user')]){
utils.takeDatabaseDumpAndGzip("${env.RELEASE_CURRENT_DB}", "biomodels", "after", "${env.RELEASE_SERVER}")
}
try {
sh "sudo service neo4j stop"
sh "sudo neo4j-admin dump --database=graph.db --to=biomodels_graph_database.dump"
sh "tar -zcf biomodels_graph_database.dump.tgz biomodels_graph_database.dump"
sh "rm biomodels_graph_database.dump"
} finally {
sh "sudo service neo4j start"
}
}
}
}
Expand All @@ -113,17 +167,11 @@ pipeline {
steps{
script{
def releaseVersion = utils.getReleaseVersion()

sh "sudo service neo4j stop"
sh "sudo neo4j-admin dump --database=graph.db --to=biomodels_graph_database.dump"
sh "tar -zcf biomodels_graph_database.dump.tgz biomodels_graph_database.dump"
sh "rm biomodels_graph_database.dump"
sh "sudo service neo4j start"

sh "mv logs biomodels-logs"

sh "mv biomodels-mapper/logs biomodels-mapper-logs"
sh "cp biomodels-mapper/output/models2pathways.tsv ."
def dataFiles = ["models2pathways.tsv", "analysis-core/analysis_v${releaseVersion}.bin"]
def logFiles = ["biomodels-logs/*", "biomodels-mapper/jsbml.log"]
def dataFiles = ["models2pathways.tsv", "analysis-core/output/analysis_v${releaseVersion}.bin", "biomodels_graph_database.dump.tgz"]
def logFiles = ["biomodels-mapper-logs/*", "biomodels-mapper/jsbml.log"]
def foldersToDelete = ["analysis-core*"]

utils.cleanUpAndArchiveBuildFiles("biomodels", dataFiles, logFiles, foldersToDelete)
Expand Down