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Merge branch 'hotfix-1.31.2'
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@arteymix
arteymix committed Mar 12, 2024
2 parents 14b9e3c + cb00ec9 commit 221682c
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Showing 239 changed files with 5,844 additions and 3,466 deletions.
5 changes: 4 additions & 1 deletion .editorconfig
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Original file line number Diff line number Diff line change
Expand Up @@ -41,4 +41,7 @@ indent_style=tab
indent_style=tab

[dwrServices.js]
indent_size=4
indent_size=4

[typo.css]
indent_style=tab
55 changes: 15 additions & 40 deletions .jenkins/Jenkinsfile
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,9 @@ def dataDir = '/space/gemmaData'
def deployDir = '/var/local/tomcat/gemma'
def cliDir = '/space/grp/gemma-cli'

// either hotfix or release, we only have one staging server
def stagingBranch = 'hotfix'

void setBuildStatus(String context, String message, String state) {
step([
$class: "GitHubCommitStatusSetter",
Expand All @@ -32,21 +35,21 @@ pipeline {
if (env.BRANCH_NAME == "master" && gemmaVersion.endsWith("-SNAPSHOT")) {
error("A production build must not have a -SNAPSHOT suffix.")
}
if (env.BRANCH_NAME == "development" && !gemmaVersion.endsWith("-SNAPSHOT")) {
if (env.BRANCH_NAME != "master" && !gemmaVersion.endsWith("-SNAPSHOT")) {
error("A development build must have a -SNAPSHOT suffix.")
}
if (env.BRANCH_NAME == 'development') {
dataDir = '/space/sandboxgemmaData'
}
if (env.BRANCH_NAME =~ '^(hotfix|release)-.*') {
if (env.BRANCH_NAME =~ '^' + stagingBranch + '-.*') {
dataDir = '/space/staginggemmaData'
}
if (env.BRANCH_NAME == 'master') {
deployDir = 'moe:' + deployDir
} else {
deployDir = 'chalmers:' + deployDir
}
if (env.BRANCH_NAME =~ '^(hotfix|release)-.*') {
if (env.BRANCH_NAME =~ '^' + stagingBranch + '-.*') {
deployDir += '-staging'
}
if (env.BRANCH_NAME != 'master') {
Expand All @@ -65,10 +68,7 @@ pipeline {
archiveArtifacts artifacts: '**/target/*.jar, **/target/*.war', fingerprint: true
setBuildStatus "Build", "Build #${env.BUILD_NUMBER} succeeded.", 'SUCCESS'
}
failure {
setBuildStatus "Build", "Build #${env.BUILD_NUMBER} failed.", 'ERROR'
}
unstable {
unsuccessful {
setBuildStatus "Build", "Build #${env.BUILD_NUMBER} failed.", 'FAILURE'
}
}
Expand All @@ -85,10 +85,7 @@ pipeline {
success {
setBuildStatus "Tests", "Tests for build #${env.BUILD_NUMBER} have passed.", 'SUCCESS'
}
failure {
setBuildStatus "Tests", "Tests for build #${env.BUILD_NUMBER} failed.", 'ERROR'
}
unstable {
unsuccessful {
setBuildStatus "Tests", "Tests for build #${env.BUILD_NUMBER} failed.", 'FAILURE'
}
}
Expand All @@ -105,10 +102,8 @@ pipeline {
parallel {
stage('Run slow unit tests and integration tests') {
when {
anyOf {
branch 'hotfix-*'
branch 'release-*'
branch 'development'
not {
branch 'master'
}
}
steps {
Expand All @@ -126,34 +121,17 @@ pipeline {
success {
setBuildStatus "Integration tests", "Integration tests for build #${env.BUILD_NUMBER} have passed.", 'SUCCESS'
}
failure {
setBuildStatus "Integration tests", "Integration tests for build #${env.BUILD_NUMBER} failed.", 'ERROR'
}
unstable {
unsuccessful {
setBuildStatus "Integration tests", "Integration tests for build #${env.BUILD_NUMBER} failed.", 'FAILURE'
}
}
}
stage('Deploy artifacts') {
when {
anyOf {
branch 'master'
branch 'development'
}
}
steps {
sh 'mvn -B deploy -DskipTests'
}
}
stage ('Deploy Maven website') {
when {
anyOf {
branch 'master'
branch 'hotfix-*'
branch 'release-*'
branch 'development'
}
}
steps {
sh 'mvn -B site-deploy'
sh "ln -Tsf ${siteDir}/gemma/gemma-${gemmaVersion} ${dataDir}/gemma-devsite"
Expand All @@ -164,8 +142,7 @@ pipeline {
when {
anyOf {
branch 'master'
branch 'hotfix-*'
branch 'release-*'
branch stagingBranch + '-*'
branch 'development'
}
}
Expand All @@ -176,10 +153,8 @@ pipeline {
}
stage ('Deploy Gemma CLI') {
when {
anyOf {
branch 'master'
branch 'hotfix-*'
branch 'release-*'
not {
branch 'development'
}
}
steps {
Expand All @@ -193,7 +168,7 @@ pipeline {
fixed {
slackSend color: 'good', message: "${env.JOB_NAME} - #${env.BUILD_NUMBER} Back to normal (<${env.BUILD_URL}|Open>)"
}
unstable {
unsuccessful {
slackSend color: 'danger', message: "${env.JOB_NAME} - #${env.BUILD_NUMBER} Failure (<${env.BUILD_URL}|Open>)"
}
}
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2 changes: 1 addition & 1 deletion gemma-cli/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<parent>
<artifactId>gemma</artifactId>
<groupId>gemma</groupId>
<version>1.31.1</version>
<version>1.31.2</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>gemma-cli</artifactId>
Expand Down
2 changes: 1 addition & 1 deletion gemma-cli/src/main/config/bash_completion.d/gemma-cli
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ function __gemma_cli_complete() {
current_option="${COMP_WORDS[$COMP_CWORD-1]}"
if ! [[ " $words " =~ ' '(affyFromCel|pubmedSearchAndSave|gwasDownload|migrateFactorValues|makePlatformAnnotFiles|platformSubsumptionTest|listExternalDatabases|printExperimentalDesign|mergePlatforms|pubmedLoad|getDataMatrix|findObsoleteTerms|vectorMerge|generateDataFile|loadTaxa|rnaseqBatchInfo|platformMapSummary|loadGenesFromFile|dgaDownload|mapPlatformToGenes|probeRename|searchIndex|pubmedAssociateToExperiments|makePrivate|addGEOData|updateExternalDatabase|splitExperiment|importDesign|makeProcessedData|affyCollapse|deletePlatformElements|diffExAnalyze|omimDownload|geneUpdate|makePublic|deleteExperiments|detachSequences|dumpForNIF|updateMultifunc|deletePhenotypes|sfariDownload|platformRepeatScan|addTSVData|pca|updateGOAnnots|ctdDownload|viewExpDesigns|affyAltsUpdate|blackList|deleteDiffEx|fillBatchInfo|genericPlatform|orderVectorsByDesign|adATcleanup|replaceData|rgdDownload|runGeeq|rnaseqDataAdd|seqCleanup|listGEOData|fetchMeshTerms|evidenceImport|switchExperimentPlatform|addPlatformSequences|coexpAnalyze|blatPlatform|corrMat|updatePubMeds|loadEvidenceForClassifier|findDatasetPubs|addExternalDatabase)' ' ]]; then
if ! [[ "$current_option" =~ (--logger|-v|--verbosity|-cs|--completion-shell|-logger) ]]; then
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'-version' '--testing' '-ha' '--version' '-v' '--completion-shell' '-logger' '-testing' '--help' '--logger' '-c' '--completion' '--verbosity' '-h' '-cs' '--help-all'" -- "$2")
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'-version' '-ha' '--version' '-v' '--completion-shell' '-logger' '-testdb' '--help' '--testdb' '--logger' '-c' '--completion' '--verbosity' '-h' '-cs' '--help-all'" -- "$2")
fi
mapfile -t -O "${#COMPREPLY[@]}" COMPREPLY < <(compgen -W "'affyFromCel' 'pubmedSearchAndSave' 'gwasDownload' 'migrateFactorValues' 'makePlatformAnnotFiles' 'platformSubsumptionTest' 'listExternalDatabases' 'printExperimentalDesign' 'mergePlatforms' 'pubmedLoad' 'getDataMatrix' 'findObsoleteTerms' 'vectorMerge' 'generateDataFile' 'loadTaxa' 'rnaseqBatchInfo' 'platformMapSummary' 'loadGenesFromFile' 'dgaDownload' 'mapPlatformToGenes' 'probeRename' 'searchIndex' 'pubmedAssociateToExperiments' 'makePrivate' 'addGEOData' 'updateExternalDatabase' 'splitExperiment' 'importDesign' 'makeProcessedData' 'affyCollapse' 'deletePlatformElements' 'diffExAnalyze' 'omimDownload' 'geneUpdate' 'makePublic' 'deleteExperiments' 'detachSequences' 'dumpForNIF' 'updateMultifunc' 'deletePhenotypes' 'sfariDownload' 'platformRepeatScan' 'addTSVData' 'pca' 'updateGOAnnots' 'ctdDownload' 'viewExpDesigns' 'affyAltsUpdate' 'blackList' 'deleteDiffEx' 'fillBatchInfo' 'genericPlatform' 'orderVectorsByDesign' 'adATcleanup' 'replaceData' 'rgdDownload' 'runGeeq' 'rnaseqDataAdd' 'seqCleanup' 'listGEOData' 'fetchMeshTerms' 'evidenceImport' 'switchExperimentPlatform' 'addPlatformSequences' 'coexpAnalyze' 'blatPlatform' 'corrMat' 'updatePubMeds' 'loadEvidenceForClassifier' 'findDatasetPubs' 'addExternalDatabase'" -- "$2")
fi
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