Skip to content

Commit

Permalink
add draft section for #376
Browse files Browse the repository at this point in the history
  • Loading branch information
kltm committed May 17, 2024
1 parent 5afce55 commit 10fd55c
Showing 1 changed file with 31 additions and 0 deletions.
31 changes: 31 additions & 0 deletions Jenkinsfile
Original file line number Diff line number Diff line change
Expand Up @@ -231,6 +231,37 @@ pipeline {
// }
// }

stage('TTL pathways package') {
steps {
script {

// Setup repo.
dir('./sparql-for-pathway-go-cams') {
// Remember that git lays out into CWD.
git branch: 'main', url: 'https://github.com/geneontology/sparql-for-pathway-go-cams.git'

// Get production blazegraph.
sh 'rm -f blazegraph-production.jnl || true'
sh 'rm -f blazegraph-production.jnl.gz || true'
sh 'wget -N http://skyhook.berkeleybop.org/snapshot/products/blazegraph/blazegraph-production.jnl.gz'
sh 'gunzip blazegraph-production.jnl.gz'

// Get noctua-models checkout.
sh 'pwd'
sh 'ls -AlFrt'
sh "git clone -b $TARGET_NOCTUA_MODELS_BRANCH https://github.com/geneontology/noctua-models.git"

sh 'NOCTUA_MODELS_PATH=./noctua-models make target/pathway-like_go-cams.tar.gz'

// Port files out to skyhook snapshot.
withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY target/pathway-like_go-cams.tar.gz skyhook@skyhook.berkeleybop.org:/home/skyhook/snapshot/products/ttl/pathway-like_go-cams.tar.gz'
}
}
}
}
}

// WARNING: This stage is a hack required to work around data damage described in https://github.com/geneontology/go-site/issues/1484 and
// https://github.com/geneontology/pipeline/issues/220.
// Redownload annotations and run ontobio-parse-assocs over them in various ways.
Expand Down

0 comments on commit 10fd55c

Please sign in to comment.