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For #2093 #342

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41 changes: 21 additions & 20 deletions Jenkinsfile
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ pipeline {
///

// The branch of geneontology/go-site to use.
TARGET_GO_SITE_BRANCH = 'master'
TARGET_GO_SITE_BRANCH = 'issue-go-site-2093-metadata'
// The branch of geneontology/go-stats to use.
TARGET_GO_STATS_BRANCH = 'master'
// The branch of go-ontology to use.
Expand All @@ -32,13 +32,13 @@ pipeline {
TARGET_NOCTUA_MODELS_BRANCH = 'master'
// The people to call when things go bad. It is a comma-space
// "separated" string.
TARGET_ADMIN_EMAILS = '[email protected],[email protected],[email protected]'
TARGET_SUCCESS_EMAILS = '[email protected],[email protected],suzia@stanford.edu,[email protected]'
TARGET_ADMIN_EMAILS = '[email protected],[email protected],[email protected]'
TARGET_SUCCESS_EMAILS = '[email protected],[email protected],muruganu@usc.edu'
TARGET_RELEASE_HOLD_EMAILS = '[email protected],[email protected],[email protected],[email protected],[email protected]'
// The file bucket(/folder) combination to use.
TARGET_BUCKET = 'go-data-product-experimental'
TARGET_BUCKET = ''
// The URL prefix to use when creating site indices.
TARGET_INDEXER_PREFIX = 'http://experimental.geneontology.io'
TARGET_INDEXER_PREFIX = ''
// This variable should typically be 'TRUE', which will cause
// some additional basic checks to be made. There are some
// very exotic cases where these check may need to be skipped
Expand Down Expand Up @@ -70,27 +70,27 @@ pipeline {

// The Zenodo concept ID to use for releases (and occasionally
// master testing).
ZENODO_ARCHIVE_CONCEPT = '1170314'
ZENODO_ARCHIVE_CONCEPT = ''
// Distribution ID for the AWS CloudFront for this branch,
// used soley for invalidations. Versioned release does not
// need this as it is always a new location and the index
// upload already has an invalidation on it. For current,
// snapshot, and experimental.
AWS_CLOUDFRONT_DISTRIBUTION_ID = 'E2CDVG5YT5R4K4'
AWS_CLOUDFRONT_RELEASE_DISTRIBUTION_ID = 'E2HF1DWYYDLTQP'
AWS_CLOUDFRONT_DISTRIBUTION_ID = ''
AWS_CLOUDFRONT_RELEASE_DISTRIBUTION_ID = ''

///
/// Ontobio Validation
///
VALIDATION_ONTOLOGY_URL="http://skyhook.berkeleybop.org/master/ontology/go.json"
VALIDATION_ONTOLOGY_URL="http://skyhook.berkeleybop.org/issue-go-site-2093-metadata/ontology/go.json"

///
/// Minerva input.
///

// Minerva operating profile.
MINERVA_INPUT_ONTOLOGIES = [
"http://skyhook.berkeleybop.org/master/ontology/extensions/go-lego.owl"
"http://skyhook.berkeleybop.org/issue-go-site-2093-metadata/ontology/extensions/go-lego.owl"
].join(" ")

///
Expand All @@ -101,19 +101,19 @@ pipeline {
GOLR_SOLR_MEMORY = "128G"
GOLR_LOADER_MEMORY = "192G"
GOLR_INPUT_ONTOLOGIES = [
"http://skyhook.berkeleybop.org/master/ontology/extensions/go-amigo.owl"
"http://skyhook.berkeleybop.org/issue-go-site-2093-metadata/ontology/extensions/go-amigo.owl"
].join(" ")
GOLR_INPUT_GAFS = [
//"http://skyhook.berkeleybop.org/master/products/upstream_and_raw_data/paint_other.gaf.gz",
"http://skyhook.berkeleybop.org/master/annotations/goa_chicken.gaf.gz",
"http://skyhook.berkeleybop.org/master/annotations/goa_chicken_complex.gaf.gz",
"http://skyhook.berkeleybop.org/master/annotations/goa_uniprot_all_noiea.gaf.gz",
"http://skyhook.berkeleybop.org/master/annotations/mgi.gaf.gz",
"http://skyhook.berkeleybop.org/master/annotations/pombase.gaf.gz",
"http://skyhook.berkeleybop.org/master/annotations/wb.gaf.gz"
"http://skyhook.berkeleybop.org/issue-go-site-2093-metadata/annotations/goa_chicken.gaf.gz",
"http://skyhook.berkeleybop.org/issue-go-site-2093-metadata/annotations/goa_chicken_complex.gaf.gz",
"http://skyhook.berkeleybop.org/issue-go-site-2093-metadata/annotations/goa_uniprot_all_noiea.gaf.gz",
"http://skyhook.berkeleybop.org/issue-go-site-2093-metadata/annotations/mgi.gaf.gz",
"http://skyhook.berkeleybop.org/issue-go-site-2093-metadata/annotations/pombase.gaf.gz",
"http://skyhook.berkeleybop.org/issue-go-site-2093-metadata/annotations/wb.gaf.gz"
].join(" ")
GOLR_INPUT_PANTHER_TREES = [
"http://skyhook.berkeleybop.org/master/products/panther/arbre.tgz"
"http://skyhook.berkeleybop.org/issue-go-site-2093-metadata/products/panther/arbre.tgz"
].join(" ")

///
Expand All @@ -132,13 +132,14 @@ pipeline {
// for no rule suppression (default behavior everything), or a
// single value (practically speaking pretty much always
// "silent")
//GORULE_TAGS_TO_SUPPRESS="silent"
GORULE_TAGS_TO_SUPPRESS="silent"

// Optional. Groups to run.
RESOURCE_GROUPS="ecocyc goa mgi paint pseudocap wb"
// Optional. Datasets to skip within the resources that we
// will run (defined in the line above).
DATASET_EXCLUDES="goa_uniprot_gcrp goa_pdb goa_chicken_isoform goa_chicken_rna goa_cow goa_cow_complex goa_cow_isoform goa_cow_rna goa_dog goa_dog_complex goa_dog_isoform goa_dog_rna goa_human goa_human goa_human_complex goa_human_rna paint_cgd paint_dictybase paint_fb paint_goa_chicken paint_goa_human paint_other paint_rgd paint_sgd paint_tair paint_zfin"
DATASET_EXCLUDES=""
//DATASET_EXCLUDES="goa_uniprot_gcrp goa_pdb goa_chicken_isoform goa_chicken_rna goa_cow goa_cow_complex goa_cow_isoform goa_cow_rna goa_dog goa_dog_complex goa_dog_isoform goa_dog_rna goa_human goa_human goa_human_complex goa_human_rna paint_cgd paint_dictybase paint_fb paint_goa_chicken paint_goa_human paint_other paint_rgd paint_sgd paint_tair paint_zfin"
// Optional. This acts as an override, /if/ it's grabbed (as
// defined above).
GOA_UNIPROT_ALL_URL="http://skyhook.berkeleybop.org/goa_uniprot_short.gaf.gz"
Expand Down
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