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Jenkinsfile
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Jenkinsfile
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#!/usr/bin/env groovy
import groovy.json.JsonOutput
import java.util.Optional
import hudson.tasks.test.AbstractTestResultAction
import hudson.model.Actionable
import hudson.tasks.junit.CaseResult
import net.sf.json.JSONArray;
import net.sf.json.JSONObject;
author = ""
message = ""
channel = "#project-sequila"
sbtOpts = "'-XX:+CMSClassUnloadingEnabled -XX:MaxPermSize=2G -Xmx4G'"
def getGitAuthor = {
def commit = sh(returnStdout: true, script: 'git rev-parse HEAD')
author = sh(returnStdout: true, script: "git --no-pager show -s --format='%an' ${commit}").trim()
}
def getLastCommitMessage = {
message = sh(returnStdout: true, script: 'git log -1 --pretty=%B').trim()
}
def populateGlobalVariables = {
getLastCommitMessage()
getGitAuthor()
println author
println message
}
def notifySlack = {
JSONArray attachments = new JSONArray();
JSONObject attachment = new JSONObject();
JSONArray fields = new JSONArray();
JSONObject authorField = new JSONObject();
authorField.put("title","Author")
authorField.put("value",author)
JSONObject msgField = new JSONObject();
msgField.put("title","Last commit")
msgField.put("value",message)
JSONObject jobField = new JSONObject();
jobField.put("title","Job name")
jobField.put("value",env.JOB_NAME)
JSONObject linkField = new JSONObject();
linkField.put("title","Jenkins link")
linkField.put("value",env.BUILD_URL.replace("http://","http://www."))
JSONObject statusField = new JSONObject();
statusField.put("title","Build status")
statusField.put("value",buildStatus)
fields.add(jobField)
fields.add(authorField)
fields.add(msgField)
fields.add(linkField)
fields.add(statusField)
attachment.put('text',"Another great piece of code has been tested...");
attachment.put('fallback','Hey, Vader seems to be mad at you.');
attachment.put("fields",fields)
attachment.put('color',buildColor);
attachments.add(attachment);
slackSend(bot:false, channel: channel, attachments: attachments.toString())
}
node {
stage('Checkout') {
checkout scm
}
populateGlobalVariables()
try {
stage('Package sequila-py') {
sh 'bash -c "source /sequila/bin/activate && cd python && python3.6 setup.py sdist bdist_wheel && twine check dist/* && twine upload -r zsibio dist/* && deactivate"'
}
stage('Test Scala code') {
echo 'Testing Scala code....'
sh "SBT_OPTS=${sbtOpts} ${tool name: 'sbt-0.13.15', type: 'org.jvnet.hudson.plugins.SbtPluginBuilder$SbtInstallation'}/bin/sbt clean test"
}
stage('Package scala code') {
//echo 'Building Scala code....'
//sh "${tool name: 'sbt-0.13.15', type: 'org.jvnet.hudson.plugins.SbtPluginBuilder$SbtInstallation'}/bin/sbt package"
echo "Generating documentation"
sh "SBT_OPTS=${sbtOpts} ${tool name: 'sbt-0.13.15', type: 'org.jvnet.hudson.plugins.SbtPluginBuilder$SbtInstallation'}/bin/sbt doc"
//publishHTML([allowMissing: false, alwaysLinkToLastBuild: true, keepAll: false, reportDir: 'target/scala-2.11/api/', reportFiles: 'package.html', reportName: 'Scala Doc', reportTitles: ''])
}
stage('Publish to Nexus snapshots and dopy DAGs') {
echo "branch: ${env.BRANCH_NAME}"
echo 'Publishing to ZSI-BIO snapshots repository....'
sh "SBT_OPTS=${sbtOpts} ${tool name: 'sbt-0.13.15', type: 'org.jvnet.hudson.plugins.SbtPluginBuilder$SbtInstallation'}/bin/sbt 'set test in publish := {}' publish"
}
stage('Code stats') {
echo 'Gathering code stats....'
sh "SBT_OPTS=${sbtOpts} ${tool name: 'sbt-0.13.15', type: 'org.jvnet.hudson.plugins.SbtPluginBuilder$SbtInstallation'}/bin/sbt stats"
}
stage('Readthedocs') {
echo 'Generating readthedocs....'
publishHTML([allowMissing: false, alwaysLinkToLastBuild: false, keepAll: false, reportDir: 'docs/build/html/', reportFiles: 'index.html', reportName: 'Readthedocs', reportTitles: ''])
sh './build_docs.sh'
}
// stage('Building Docker images') {
//
// echo 'Building Docker images....'
// sh './build.sh'
//
// }
stage('Performance testing') {
sh "SBT_OPTS=${sbtOpts} ${tool name: 'sbt-0.13.15', type: 'org.jvnet.hudson.plugins.SbtPluginBuilder$SbtInstallation'}/bin/sbt 'set test in assembly := {}' assembly"
sh "ssh bdg-perf@cdh00 rm -rf /tmp/bdg-sequila-assembly-*.jar"
sh "scp target/scala-2.11/bdg-sequila-assembly-*.jar bdg-perf@cdh00:/tmp"
sh "scp performance/bdg_perf/bdg_perf_sequila.scala bdg-perf@cdh00:/tmp"
sh 'ssh bdg-perf@cdh00 ". ~/.profile; spark-shell --conf spark.sql.catalogImplementation=in-memory --conf spark.hadoop.yarn.timeline-service.enabled=false --principal bdg-perf@CL.II.PW.EDU.PL --keytab /data/work/home/bdg-perf/keytabs/bdg-perf.keytab --master=yarn-client --executor-memory=3g --num-executors=40 --executor-cores=1 --driver-memory=8g -i /tmp/bdg_perf_sequila.scala --packages org.postgresql:postgresql:42.1.1 --conf spark.biodatageeks.perf.testId=$BRANCH_NAME --jars /tmp/bdg-sequila-assembly-*.jar -v"'
sh './build_perf_report.sh'
}
}
catch (e){currentBuild.result="FAIL"}
stage('Notify'){
junit '**/target/test-reports/*.xml'
buildColor = currentBuild.result == null ? "good" : "danger"
buildStatus = currentBuild.result == null ? "SUCCESS:clap:" : currentBuild.result+":cry:"
notifySlack()
}
}