diff --git a/Jenkinsfile b/Jenkinsfile index 81e1bec..b5ab2a0 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -17,7 +17,7 @@ pipeline { /// // The branch of geneontology/go-site to use. - TARGET_GO_SITE_BRANCH = 'master' + TARGET_GO_SITE_BRANCH = 'issue-2364-panther-19' // The branch of geneontology/go-stats to use. TARGET_GO_STATS_BRANCH = 'master' // The branch of go-ontology to use. @@ -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 = 'sjcarbon@lbl.gov,debert@usc.edu,smoxon@lbl.gov' - TARGET_SUCCESS_EMAILS = 'sjcarbon@lbl.gov,debert@usc.edu,suzia@stanford.edu,smoxon@lbl.gov' - TARGET_RELEASE_HOLD_EMAILS = 'sjcarbon@lbl.gov,debert@usc.edu,pascale.gaudet@sib.swiss,pgaudet1@gmail.com,smoxon@lbl.gov' + TARGET_ADMIN_EMAILS = 'debert@usc.edu' + TARGET_SUCCESS_EMAILS = 'debert@usc.edu' + TARGET_RELEASE_HOLD_EMAILS = 'debert@usc.edu' // The file bucket(/folder) combination to use. - TARGET_BUCKET = 'go-data-product-experimental' + TARGET_BUCKET = 'null' // The URL prefix to use when creating site indices. - TARGET_INDEXER_PREFIX = 'http://experimental.geneontology.io' + TARGET_INDEXER_PREFIX = 'null' // 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 @@ -62,7 +62,7 @@ pipeline { /// PANTHER/PAINT metadata. /// - PANTHER_VERSION = '17.0' + PANTHER_VERSION = '19.0' /// /// Application tokens. @@ -70,19 +70,19 @@ pipeline { // The Zenodo concept ID to use for releases (and occasionally // master testing). - ZENODO_ARCHIVE_CONCEPT = '1170314' + ZENODO_ARCHIVE_CONCEPT = 'null' // 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 = 'null' + AWS_CLOUDFRONT_RELEASE_DISTRIBUTION_ID = 'null' /// /// Ontobio Validation /// - VALIDATION_ONTOLOGY_URL="http://skyhook.berkeleybop.org/master/ontology/go.json" + VALIDATION_ONTOLOGY_URL="http://skyhook.berkeleybop.org/go-site-2364-panther-19/ontology/go.json" /// /// Minerva input. @@ -90,7 +90,7 @@ pipeline { // Minerva operating profile. MINERVA_INPUT_ONTOLOGIES = [ - "http://skyhook.berkeleybop.org/master/ontology/extensions/go-lego.owl" + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/ontology/extensions/go-lego.owl" ].join(" ") /// @@ -101,19 +101,37 @@ 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/go-site-2364-panther-19/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/go-site-2364-panther-19/products/upstream_and_raw_data/paint_other.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/cgd.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/dictybase.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/ecocyc.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/fb.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/genedb_lmajor.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/genedb_tbrucei.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/genedb_pfalciparum.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/goa_chicken.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/goa_cow.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/goa_dog.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/goa_human.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/goa_pig.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/goa_uniprot_all_noiea.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/japonicusdb.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/mgi.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/pombase.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/pseudocap.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/rgd.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/sgd.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/sgn.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/tair.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/wb.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/xenbase.gaf.gz", + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/annotations/zfin.gaf.gz" ].join(" ") GOLR_INPUT_PANTHER_TREES = [ - "http://skyhook.berkeleybop.org/master/products/panther/arbre.tgz" + "http://skyhook.berkeleybop.org/go-site-2364-panther-19/products/panther/arbre.tgz" ].join(" ") /// @@ -132,16 +150,16 @@ 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" + // RESOURCE_GROUPS="" // 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="" // 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" + // GOA_UNIPROT_ALL_URL="" } options{