Skip to content

Commit

Permalink
full version with all parts and email opetational #305
Browse files Browse the repository at this point in the history
  • Loading branch information
@kltm
kltm committed Aug 25, 2023
1 parent 3572fcc commit 54f4322
Showing 1 changed file with 71 additions and 82 deletions.
153 changes: 71 additions & 82 deletions Jenkinsfile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -159,61 +159,61 @@ pipeline {
cleanWs deleteDirs: true, disableDeferredWipeout: true
}
}
// stage('Initialize') {
// steps {

// ///
// /// Automatic run variables.
// ///

// // Pin dates and day to beginning of run.
// script {
// env.START_DATE = sh (
// script: 'date +%Y-%m-%d',
// returnStdout: true
// ).trim()

// env.START_DAY = sh (
// script: 'date +%A',
// returnStdout: true
// ).trim()
// }

// // Reset base.
// initialize();

// sh 'env > env.txt'
// sh 'echo $BRANCH_NAME > branch.txt'
// sh 'echo "$BRANCH_NAME"'
// sh 'cat env.txt'
// sh 'cat branch.txt'
// sh 'echo $START_DAY > dow.txt'
// sh 'echo "$START_DAY"'
// sh 'echo $START_DATE > date.txt'
// sh 'echo "$START_DATE"'
// }
// }
// // Download GAFs from datasets.yaml in go-site and then upload
// // to skyhook in their appropriate locations.
// stage("Download annotation data") {
// steps {
// dir("./go-site") {
// git branch: TARGET_GO_SITE_BRANCH, url: 'https://github.com/geneontology/go-site.git'

// script {

// sh "grep -r 'ftp.ebi.ac.uk' ./metadata/datasets/ | grep -oh 'https:.*' > ./files.txt"
// sh "sed -e 's/https/ftp/g' ./files.txt > ./files.txt.changed"
// sh "time wget -i ./files.txt.changed -P ./copy"
// }

// withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
// // Upload to skyhook to the expected location.
// sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" ./copy/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/upstream_and_raw_data/'
// }
// }
// }
// }
stage('Initialize') {
steps {

///
/// Automatic run variables.
///

// Pin dates and day to beginning of run.
script {
env.START_DATE = sh (
script: 'date +%Y-%m-%d',
returnStdout: true
).trim()

env.START_DAY = sh (
script: 'date +%A',
returnStdout: true
).trim()
}

// Reset base.
initialize();

sh 'env > env.txt'
sh 'echo $BRANCH_NAME > branch.txt'
sh 'echo "$BRANCH_NAME"'
sh 'cat env.txt'
sh 'cat branch.txt'
sh 'echo $START_DAY > dow.txt'
sh 'echo "$START_DAY"'
sh 'echo $START_DATE > date.txt'
sh 'echo "$START_DATE"'
}
}
// Download GAFs from datasets.yaml in go-site and then upload
// to skyhook in their appropriate locations.
stage("Download annotation data") {
steps {
dir("./go-site") {
git branch: TARGET_GO_SITE_BRANCH, url: 'https://github.com/geneontology/go-site.git'

script {

sh "grep -r 'ftp.ebi.ac.uk' ./metadata/datasets/ | grep -oh 'https:.*' > ./files.txt"
sh "sed -e 's/https/ftp/g' ./files.txt > ./files.txt.changed"
sh "time wget -i ./files.txt.changed -P ./copy"
}

withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) {
// Upload to skyhook to the expected location.
sh 'rsync -avz -e "ssh -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY" ./copy/* skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/products/upstream_and_raw_data/'
}
}
}
}
stage('Publish') {
when { anyOf { branch 'goa-copy-to-mirror' } }
steps {
Expand Down Expand Up @@ -271,33 +271,22 @@ pipeline {
}
}
}
// post {
// // Let's let our people know if things go well.
// success {
// script {
// if( env.BRANCH_NAME == 'release' ){
// echo "There has been a successful run of the ${env.BRANCH_NAME} pipeline."
// emailext to: "${TARGET_SUCCESS_EMAILS}",
// subject: "GO Pipeline success for ${env.BRANCH_NAME}",
// body: "There has been successful run of the ${env.BRANCH_NAME} pipeline. Please see: https://build.geneontology.org/job/geneontology/job/pipeline/job/${env.BRANCH_NAME}"
// }
// }
// }
// // Let's let our internal people know if things change.
// changed {
// echo "There has been a change in the ${env.BRANCH_NAME} pipeline."
// emailext to: "${TARGET_ADMIN_EMAILS}",
// subject: "GO Pipeline change for ${env.BRANCH_NAME}",
// body: "There has been a pipeline status change in ${env.BRANCH_NAME}. Please see: https://build.geneontology.org/job/geneontology/job/pipeline/job/${env.BRANCH_NAME}"
// }
// // Let's let our internal people know if things go badly.
// failure {
// echo "There has been a failure in the ${env.BRANCH_NAME} pipeline."
// emailext to: "${TARGET_ADMIN_EMAILS}",
// subject: "GO Pipeline FAIL for ${env.BRANCH_NAME}",
// body: "There has been a pipeline failure in ${env.BRANCH_NAME}. Please see: https://build.geneontology.org/job/geneontology/job/pipeline/job/${env.BRANCH_NAME}"
// }
// }
post {
// Let's let our internal people know if things change.
changed {
echo "There has been a change in the ${env.BRANCH_NAME} pipeline."
emailext to: "${TARGET_ADMIN_EMAILS}",
subject: "GO Pipeline change for ${env.BRANCH_NAME}",
body: "There has been a pipeline status change in ${env.BRANCH_NAME}. Please see: https://build.geneontology.org/job/geneontology/job/pipeline/job/${env.BRANCH_NAME}"
}
// Let's let our internal people know if things go badly.
failure {
echo "There has been a failure in the ${env.BRANCH_NAME} pipeline."
emailext to: "${TARGET_ADMIN_EMAILS}",
subject: "GO Pipeline FAIL for ${env.BRANCH_NAME}",
body: "There has been a pipeline failure in ${env.BRANCH_NAME}. Please see: https://build.geneontology.org/job/geneontology/job/pipeline/job/${env.BRANCH_NAME}"
}
}
}

// Check that we do not affect public targets on non-mainline runs.
Expand Down

0 comments on commit 54f4322

Please sign in to comment.