From 3567af27fd3affbb828684eba40e1397f6ecb72f Mon Sep 17 00:00:00 2001 From: Guthrie Price Date: Mon, 4 Nov 2024 14:38:38 -0800 Subject: [PATCH] Add source record URLs to provenance --- assets/biolink-model/common/infores-catalog-v0.2.8.json | 1 - assets/biolink-model/common/infores-catalog-v0.2.9.json | 2 +- .../biolink-model/common/infores-catalog-v0.2.9.json.bkup | 1 + lib/biolink-model.mjs | 3 ++- lib/trapi.mjs | 7 ++++--- utilities/node/inforesToInforesMini.mjs | 2 +- 6 files changed, 9 insertions(+), 7 deletions(-) delete mode 100644 assets/biolink-model/common/infores-catalog-v0.2.8.json create mode 100644 assets/biolink-model/common/infores-catalog-v0.2.9.json.bkup diff --git a/assets/biolink-model/common/infores-catalog-v0.2.8.json b/assets/biolink-model/common/infores-catalog-v0.2.8.json deleted file mode 100644 index 178fb260..00000000 --- a/assets/biolink-model/common/infores-catalog-v0.2.8.json +++ /dev/null @@ -1 +0,0 @@ -{"infores:agrkb":{"name":"Alliance of Genome 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API","url":"https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-APIs","knowledge_level":"trusted"},"infores:tissues":{"name":"TISSUES","url":"https://github.com/NCATSTranslator/Translator-All/wiki/TISSUES","knowledge_level":"unknown"},"infores:biothings-tissues":{"name":"BioThings TISSUES API","url":"https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-APIs","knowledge_level":"unknown"},"infores:mygeneset-info":{"name":"MyGeneset.info API","url":"https://github.com/NCATSTranslator/Translator-All/wiki/MyGeneset","knowledge_level":"unknown"}} diff --git a/lib/biolink-model.mjs b/lib/biolink-model.mjs index e4af4c1f..5826a913 100644 --- a/lib/biolink-model.mjs +++ b/lib/biolink-model.mjs @@ -60,10 +60,11 @@ export function deprecatedPredicateToPredicateAndQualifiers(predicate) { } export function inforesToProvenance(infores) { - const provenance = INFORES_CATALOG[infores]; + const provenance = INFORES_CATALOG[infores.id]; if (!provenance) { return false; } + provenance.records = infores.records; return provenance; } diff --git a/lib/trapi.mjs b/lib/trapi.mjs index 113020cd..b7716529 100644 --- a/lib/trapi.mjs +++ b/lib/trapi.mjs @@ -192,7 +192,7 @@ export function creativeAnswersToSummary (qid, answers, maxHops) { const queryType = answerToQueryType(answers[0]); function agentToName(agent) { - return bl.inforesToProvenance(agent).name; + return bl.inforesToProvenance({'id': agent, 'records': []}).name; } const [sfs, errors] = creativeAnswersToSummaryFragments(answers, nodeRules, edgeRules, maxHops); @@ -589,14 +589,15 @@ function getPublications() { } function getPrimarySource(sources) { -for (let source of sources) { + for (let source of sources) { const id = cmn.jsonGet(source, 'resource_id', false); const role = cmn.jsonGet(source, 'resource_role', false); + const records = cmn.jsonGet(source, 'source_record_urls', []); if (!role || !id) { continue; } else if (role === 'primary_knowledge_source') { - return [id]; + return [{'id': id, 'records': records}]; } } diff --git a/utilities/node/inforesToInforesMini.mjs b/utilities/node/inforesToInforesMini.mjs index c6cbe29b..5ccca0a4 100644 --- a/utilities/node/inforesToInforesMini.mjs +++ b/utilities/node/inforesToInforesMini.mjs @@ -26,7 +26,7 @@ inforesEntries.forEach((inforesEntry) => { { inforesMini[inforesEntry.id] = { name: inforesEntry.name || inforesEntry.id, - url: (inforesEntry.xref && inforesEntry.xref.length > 0) ? inforesEntry.xref[0] : null, + wiki: (inforesEntry.xref && inforesEntry.xref.length > 0) ? inforesEntry.xref[0] : null, knowledge_level: cleanupKnowledgeLevel(inforesEntry['knowledge level']) }; }