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Add source record URLs to provenance #243

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Add source record URLs to provenance #243

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1 change: 0 additions & 1 deletion assets/biolink-model/common/infores-catalog-v0.2.8.json
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2 changes: 1 addition & 1 deletion assets/biolink-model/common/infores-catalog-v0.2.9.json
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1 change: 1 addition & 0 deletions assets/biolink-model/common/infores-catalog-v0.2.9.json.bkup
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3 changes: 2 additions & 1 deletion lib/biolink-model.mjs
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
}

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7 changes: 4 additions & 3 deletions lib/trapi.mjs
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down Expand Up @@ -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}];
}
}

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2 changes: 1 addition & 1 deletion utilities/node/inforesToInforesMini.mjs
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Original file line number Diff line number Diff line change
Expand Up @@ -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'])
};
}
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