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add in rudamentry neo build, but not deploy (@cmungall); some small f…
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…ixes; work on #35
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@kltm
kltm committed Jan 24, 2019
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Expand Up @@ -159,135 +159,62 @@ pipeline {
// Build owltools and get it into the shared filesystem.
stage('Ready production software') {
steps {
parallel(
"Ready owltools": {
// Legacy: build 'owltools-build'
dir('./owltools') {
// Remember that git lays out into CWD.
git 'https://github.com/owlcollab/owltools.git'
sh 'mvn -f OWLTools-Parent/pom.xml -U clean install -DskipTests -Dmaven.javadoc.skip=true -Dsource.skip=true'
// Attempt to rsync produced into bin/.
withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" OWLTools-Runner/target/owltools [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" OWLTools-Oort/bin/* [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" OWLTools-NCBI/bin/* [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
sh 'rsync -vhac -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" --exclude ".git" OWLTools-Oort/reporting/* [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
sh 'rsync -vhac -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" --exclude ".git" OWLTools-Runner/contrib/* [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
}
}
}//,
// "Ready minerva": {
// dir('./minerva') {
// // Remember that git lays out into CWD.
// git 'https://github.com/geneontology/minerva.git'
// sh './build-cli.sh'
// // Attempt to rsync produced into bin/.
// withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
// sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" minerva-cli/bin/minerva-cli.* [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
// }
// }
// },
// "Ready robot": {
// // Legacy: build 'robot-build'
// dir('./robot') {
// git 'https://github.com/ontodev/robot.git'
// // Update the POMs by replacing "SNAPSHOT"
// // with the current Git hash. First make
// // sure maven-help-plugin is installed
// sh 'mvn org.apache.maven.plugins:maven-help-plugin:2.1.1:evaluate -Dexpression=project.version'
// // Now get and set the version.
// // Originally: sh 'VERSION=`mvn org.apache.maven.plugins:maven-help-plugin:2.1.1:evaluate -Dexpression=project.version | grep -v '\[' | sed 's/-SNAPSHOT//'`'
// sh 'VERSION=`mvn org.apache.maven.plugins:maven-help-plugin:2.1.1:evaluate -Dexpression=project.version | grep -v \'\\[\' | sed \'s/-SNAPSHOT//\'`'
// sh 'BUILD=`git rev-parse --short HEAD`'
// sh 'mvn versions:set -DnewVersion=$VERSION+$BUILD'
// sh 'mvn -U clean install -DskipTests'
// // Attempt to rsync produced into bin/.
// withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
// sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" bin/* [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
// }
// }
// },
// "Ready arachne": {
// dir('./arachne') {
// sh 'wget -N https://github.com/balhoff/arachne/releases/download/v1.0.2/arachne-1.0.2.tgz'
// sh 'tar -xvf arachne-1.0.2.tgz'
// // Attempt to rsync produced into bin/.
// withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
// sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" arachne-1.0.2/bin/* [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
// // WARNING/BUG: needed for arachne to
// // run at this point.
// sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" arachne-1.0.2/lib/* [email protected]:/home/skyhook/$BRANCH_NAME/lib/'
// }
// }
// },
// "Ready blazegraph-runner": {
// dir('./blazegraph-runner') {
// sh 'wget -N https://github.com/balhoff/blazegraph-runner/releases/download/v1.4/blazegraph-runner-1.4.tgz'
// sh 'tar -xvf blazegraph-runner-1.4.tgz'
// withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
// // Attempt to rsync bin into bin/.
// sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" blazegraph-runner-1.4/bin/* [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
// // Attempt to rsync libs into lib/.
// sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" blazegraph-runner-1.4/lib/* [email protected]:/home/skyhook/$BRANCH_NAME/lib/'
// }
// }
// }
)
// Legacy: build 'owltools-build'
dir('./owltools') {
// Remember that git lays out into CWD.
git 'https://github.com/owlcollab/owltools.git'
sh 'mvn -f OWLTools-Parent/pom.xml -U clean install -DskipTests -Dmaven.javadoc.skip=true -Dsource.skip=true'
// Attempt to rsync produced into bin/.
withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" OWLTools-Runner/target/owltools [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" OWLTools-Oort/bin/* [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" OWLTools-NCBI/bin/* [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
sh 'rsync -vhac -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" --exclude ".git" OWLTools-Oort/reporting/* [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
sh 'rsync -vhac -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" --exclude ".git" OWLTools-Runner/contrib/* [email protected]:/home/skyhook/$BRANCH_NAME/bin/'
}
}
}
}
// // See https://github.com/geneontology/go-ontology for details
// // on the ontology release pipeline. This ticket runs
// // daily(TODO?) and creates all the files normally included in
// // a release, and deploys to S3.
// stage('Produce ontology') {
// agent {
// docker {
// image 'obolibrary/odkfull:v1.1.7'
// // Reset Jenkins Docker agent default to original
// // root.
// args '-u root:root'
// }
// }
// steps {
// // Create a relative working directory and setup our
// // data environment.
// dir('./go-ontology') {
// git 'https://github.com/geneontology/go-ontology.git'
// See https://github.com/geneontology/go-ontology for details
// on the ontology release pipeline. This ticket runs
// daily(TODO?) and creates all the files normally included in
// a release, and deploys to S3.
stage('Produce ontology') {
steps {
// Create a relative working directory and setup our
// data environment.
dir('./neo') {
git 'https://github.com/geneontology/neo.git'

// // Default namespace.
// sh 'OBO=http://purl.obolibrary.org/obo'
// Default namespace.
sh 'OBO=http://purl.obolibrary.org/obo'

// dir('./src/ontology') {
// retry(3){
// sh 'make all'
// }
// retry(3){
// sh 'make prepare_release'
// }
// }
// Make all software products available in bin/.
sh 'mkdir -p bin/'
withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" [email protected]:/home/skyhook/$BRANCH_NAME/bin/* ./bin/'
}
sh 'chmod +x bin/*'

// // Make sure that we copy any files there,
// // including the core dump of produced.
// withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
// //sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" target/* [email protected]:/home/skyhook/$BRANCH_NAME/ontology'
// sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -r target/* [email protected]:/home/skyhook/$BRANCH_NAME/ontology/'
// }
//
withEnv(['PATH+EXTRA=:bin:./bin']){
retry(3){
sh 'make clean all'
}
}

// // Now that the files are safely away onto skyhook for
// // debugging, test for the core dump.
// script {
// if( WE_ARE_BEING_SAFE_P == 'TRUE' ){
// Make sure that we copy any files there,
// including the core dump of produced.
withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY neo.obo neo.owl [email protected]:/home/skyhook/$BRANCH_NAME/ontology/'
}

// def found_core_dump_p = fileExists 'target/core_dump.owl'
// if( found_core_dump_p ){
// error 'ROBOT core dump detected--bailing out.'
// }
// }
// }
// }
// }
// }
//...
// TODO: Future deplyment like?
// s3cmd -c ~/.s3cfg.go-push --acl-public --reduced-redundancy --mime-type=application/rdf+xml put neo.obo neo.owl s3://go-build/$JOB_BASE_NAME/latest/
}
}
}
/./..
stage('Produce derivatives') {
agent {
docker {
Expand All @@ -314,12 +241,12 @@ pipeline {
}
}
}
//...
stage('Sanity II') {
steps {
echo 'TODO: Sanity II'
}
}
// //...
// stage('Sanity II') {
// steps {
// echo 'TODO: Sanity II'
// }
// }
// stage('TODO: Final status') {
// steps {
// echo 'TODO: final'
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