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attempt at full command; work on #158
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@@ -349,7 +349,7 @@ pipeline { | |
| git 'https://github.com/geneontology/go-ontology.git' | ||
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| // Default namespace. | ||
| sh 'env' | ||
| sh 'env' | ||
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| dir('./src/ontology') { | ||
| retry(3){ | ||
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@@ -376,54 +376,49 @@ pipeline { | |
| if( found_core_dump_p ){ | ||
| error 'ROBOT core dump detected--bailing out.' | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| // Attempt to use pathways2GO release. | ||
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| // TODO: here. | ||
| } | ||
| } | ||
| } | ||
| stage('Make Noctua GPAD') { | ||
| steps { | ||
| // May be parallelized in the future, but may need to | ||
| // serve as input into into mega step. | ||
| script { | ||
| stage('Produce ontology') { | ||
| // agent { | ||
| // docker { | ||
| // image 'obolibrary/odkfull:v1.1.7' | ||
| // // Reset Jenkins Docker agent default to original | ||
| // // root. | ||
| // args '-u root:root' | ||
| // } | ||
| // } | ||
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| dir('./noctua-models') { | ||
| git url: 'https://github.com/geneontology/noctua-models.git' | ||
| // Attempt to use pathways2GO release. | ||
| // Create a relative working directory and setup our | ||
| // data environment. | ||
| dir('./pathways2GO') { | ||
| git 'https://github.com/geneontology/pathways2GO.git' | ||
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| // Make all software products available in bin/ | ||
| // (and lib/). | ||
| sh 'mkdir -p bin/' | ||
| sh 'mkdir -p lib/' | ||
| 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/' | ||
| // WARNING/BUG: needed for blazegraph-runner | ||
| // to run at this point. | ||
| sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" [email protected]:/home/skyhook/$BRANCH_NAME/lib/* ./lib/' | ||
| } | ||
| sh 'chmod +x bin/*' | ||
| // Default namespace. | ||
| sh 'env' | ||
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| // Compile models. | ||
| sh 'mkdir -p legacy/gpad' | ||
| withEnv(['MINERVA_CLI_MEMORY=128G']){ | ||
| // "Import" models. | ||
| sh './bin/minerva-cli.sh --import-owl-models -f models -j blazegraph.jnl' | ||
| // Convert GO-CAM to GPAD. | ||
| sh './bin/minerva-cli.sh --lego-to-gpad-sparql --ontology $MINERVA_INPUT_ONTOLOGIES -i blazegraph.jnl --gpad-output legacy/gpad' | ||
| } | ||
| retry(3){ | ||
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| // Collation. | ||
| sh 'perl ./util/collate-gpads.pl legacy/gpad/*.gpad' | ||
| // Get jar. | ||
| sh 'wget -N https://github.com/geneontology/pathways2GO/releases/download/v0.1.0/biopax2go.jar' | ||
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| // Rename, compress, and move to skyhook. | ||
| sh 'mcp "legacy/*.gpad" "legacy/noctua_#1.gpad"' | ||
| sh 'gzip -vk legacy/noctua_*.gpad' | ||
| withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) { | ||
| sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY legacy/noctua_*.gpad.gz [email protected]:/home/skyhook/$BRANCH_NAME/products/annotations/' | ||
| } | ||
| // Biopax files needed | ||
| sh 'wget -N https://reactome.org/download/current/biopax.zip' | ||
| sh 'gunzip biopax.zip' | ||
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| // The actual command. | ||
| sh 'java -jar biopax2go.jar -b Homo-sapiens.owl -reacto ./REACTO -c catalog-v001-for-noctua.xml -lego http://skyhook.berkeleybop.org/issue-158-reactome-ontology/ontology/extensions/go-lego.owl' | ||
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| // Fake Catalog. | ||
| sh 'touch catalog-v001-for-noctua.xml' | ||
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| // Make sure that we copy any files there, | ||
| // including the core dump of produced. | ||
| withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) { | ||
| sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -r ./REACTO/* [email protected]:/home/skyhook/$BRANCH_NAME/ontology/extensions/' | ||
| } | ||
| } | ||
| } | ||
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