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Modify Jenkinsfile to use new go-amigo.owl #322

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Modify Jenkinsfile to use new go-amigo.owl #322

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46 changes: 3 additions & 43 deletions Jenkinsfile
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Original file line number Diff line number Diff line change
Expand Up @@ -122,24 +122,7 @@ pipeline {
GOLR_SOLR_MEMORY = "128G"
GOLR_LOADER_MEMORY = "192G"
GOLR_INPUT_ONTOLOGIES = [
"http://skyhook.berkeleybop.org/go-ontology-dev/ontology/extensions/go-gaf.owl",
"http://skyhook.berkeleybop.org/go-ontology-dev/ontology/extensions/gorel.owl",
"http://skyhook.berkeleybop.org/go-ontology-dev/ontology/extensions/go-modules-annotations.owl",
"http://skyhook.berkeleybop.org/go-ontology-dev/ontology/extensions/go-taxon-subsets.owl",
"http://purl.obolibrary.org/obo/eco/eco-basic.owl",
"http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl",
// BUG: Temporarily lock in CL version; see:
// https://github.com/geneontology/go-ontology/issues/23510
//"http://purl.obolibrary.org/obo/cl/cl-basic.owl",
"http://purl.obolibrary.org/obo/cl/releases/2022-02-16/cl-basic.owl",
"http://purl.obolibrary.org/obo/pato.owl",
"http://purl.obolibrary.org/obo/po.owl",
"http://purl.obolibrary.org/obo/chebi.owl",
// BUG: Temporarily lock in uberon version; see:
// https://github.com/geneontology/go-ontology/issues/23468
//"http://purl.obolibrary.org/obo/uberon/basic.owl",
"http://purl.obolibrary.org/obo/uberon/releases/2022-05-17/uberon-basic.owl",
"http://purl.obolibrary.org/obo/wbbt.owl"
"http://skyhook.berkeleybop.org/go-ontology-dev/ontology/extensions/go-amigo.owl"
].join(" ")
GOLR_INPUT_GAFS = [
//"http://skyhook.berkeleybop.org/go-ontology-dev/products/annotations/paint_other.gaf.gz",
Expand Down Expand Up @@ -416,34 +399,11 @@ pipeline {
sh 'echo `date` | cat - ./unsatisfiable_explanations.md > ./unsatisfiable_explanations.md.tmp && mv -f ./unsatisfiable_explanations.md.tmp ./unsatisfiable_explanations.md'
}

// Only continue with the "deep" check if
// there was not a surface issue.
// Check go-amigo if there was not an issue with go-lego
if( ONTOLOGY_ERROR_BUILD_P == 'FALSE' ){
// Try and run robot no matter what, as
// sometimes the ontology can build but
// there are still errors.
sh 'rm -f eco-basic.owl || true'
sh 'rm -f taxslim.owl || true'
sh 'rm -f cl-basic.owl || true'
sh 'rm -f pato.owl || true'
sh 'rm -f po.owl || true'
sh 'rm -f chebi.owl || true'
sh 'rm -f basic.owl || true'
sh 'rm -f wbbt.owl || true'
sh 'wget http://purl.obolibrary.org/obo/eco/eco-basic.owl'
sh 'wget http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl'
sh 'wget http://purl.obolibrary.org/obo/cl/cl-basic.owl'
sh 'wget http://purl.obolibrary.org/obo/pato.owl'
sh 'wget http://purl.obolibrary.org/obo/po.owl'
sh 'wget http://purl.obolibrary.org/obo/chebi.owl'
sh 'wget http://purl.obolibrary.org/obo/uberon/basic.owl'
sh 'wget http://purl.obolibrary.org/obo/wbbt.owl'
sh 'rm -f merged.owl || true'
sh 'robot merge -i eco-basic.owl -i taxslim.owl -i cl-basic.owl -i pato.owl -i po.owl -i chebi.owl -i basic.owl -i wbbt.owl -i ./extensions/go-gaf.owl -i ./extensions/gorel.owl -i ./extensions/go-modules-annotations.owl -i ./extensions/go-taxon-subsets.owl -o merged.owl'
sh 'robot explain -i ./merged.owl -M unsatisfiability --unsatisfiable random:2 --explanation ./unsatisfiable_explanations_full.md'
sh 'robot --catalog ./catalog-v001.xml explain -i ./extensions/go-amigo-edit.ofn -M unsatisfiability --unsatisfiable random:2 --explanation ./unsatisfiable_explanations.md'
sh 'echo $BUILD_ID | cat - ./unsatisfiable_explanations_full.md > ./unsatisfiable_explanations_full.md.tmp && mv -f ./unsatisfiable_explanations_full.md.tmp ./unsatisfiable_explanations_full.md'
sh 'echo `date` | cat - ./unsatisfiable_explanations_full.md > ./unsatisfiable_explanations_full.md.tmp && mv -f ./unsatisfiable_explanations_full.md.tmp ./unsatisfiable_explanations_full.md'

// Check explanations.
try {
sh 'grep "No explanations found" ./unsatisfiable_explanations_full.md'
Expand Down