diff --git a/Jenkinsfile b/Jenkinsfile index f7a47a0..7b2fec7 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -329,59 +329,60 @@ pipeline { ) } } - // // 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 Gene 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 (GO)') { + 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' + + // Default namespace. + sh 'env' - // // Default namespace. - // sh 'env' + dir('./src/ontology') { + retry(3){ + sh 'make RELEASEDATE=$START_DATE OBO=http://purl.obolibrary.org/obo ROBOT_ENV="ROBOT_JAVA_ARGS=-Xmx48G" all' + } + retry(3){ + sh 'make prepare_release' + } + } - // dir('./src/ontology') { - // retry(3){ - // sh 'make RELEASEDATE=$START_DATE OBO=http://purl.obolibrary.org/obo ROBOT_ENV="ROBOT_JAVA_ARGS=-Xmx48G" all' - // } - // retry(3){ - // sh 'make prepare_release' - // } - // } + // 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=$SKYHOOK_IDENTITY" target/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/ontology' + sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -r target/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/ontology/' + } - // // 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=$SKYHOOK_IDENTITY" target/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/ontology' - // sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -r target/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/ontology/' - // } + // Now that the files are safely away onto skyhook for + // debugging, test for the core dump. + script { + if( WE_ARE_BEING_SAFE_P == 'TRUE' ){ - // // Now that the files are safely away onto skyhook for - // // debugging, test for the core dump. - // script { - // if( WE_ARE_BEING_SAFE_P == 'TRUE' ){ + def found_core_dump_p = fileExists 'target/core_dump.owl' + if( found_core_dump_p ){ + error 'ROBOT core dump detected--bailing out.' + } + } + } + } + } + } - // def found_core_dump_p = fileExists 'target/core_dump.owl' - // if( found_core_dump_p ){ - // error 'ROBOT core dump detected--bailing out.' - // } - // } - // } - // } - // } - // } - stage('Produce Reactome Ontology') { + stage('Produce ontology (Reactome)') { // agent { // docker { // image 'obolibrary/odkfull:v1.1.7' @@ -422,7 +423,7 @@ pipeline { // 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=$SKYHOOK_IDENTITY -r ./reacto.owl skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/ontology/extensions/' + sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -r ./reacto.owl skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/ontology/extensions/reacto.owl' } } }