-
Notifications
You must be signed in to change notification settings - Fork 5
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
1 changed file
with
50 additions
and
49 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -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=$SKYHOOK_IDENTITY" target/* [email protected]:/home/skyhook/$BRANCH_NAME/ontology' | ||
| sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -r target/* [email protected]:/home/skyhook/$BRANCH_NAME/ontology/' | ||
| } | ||
|
|
||
| // // 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/' | ||
| // } | ||
| // 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=$SKYHOOK_IDENTITY -r ./reacto.owl [email protected]:/home/skyhook/$BRANCH_NAME/ontology/extensions/' | ||
| sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -r ./reacto.owl [email protected]:/home/skyhook/$BRANCH_NAME/ontology/extensions/reacto.owl' | ||
| } | ||
| } | ||
| } | ||
|
|
||