Merge branch 'main' of https://github.com/biothings/bte_trapi_query_g…

…raph_handler into dev
biothings · Nov 4, 2024 · 2a772fe · 2a772fe
2 parents c0560dd + 9eabfa1
commit 2a772fe
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Showing 3 changed files with 2 additions and 29 deletions.
diff --git a/src/graph/kg_edge.ts b/src/graph/kg_edge.ts
@@ -120,8 +120,7 @@ export default class KGEdge {
   addAdditionalAttributes(name: string, value: string | string[] | TrapiAttribute[]): void {
     // special handling for full edge attributes
     if (name === 'edge-attributes') {
-      if (this.attributes[name]) this.attributes[name] = [...this.attributes[name], ...value as TrapiAttribute[]];
-      else this.attributes[name] = value as TrapiAttribute[];
+      this.attributes[name] = value as TrapiAttribute[];
       return;
     }
 

diff --git a/src/graph/knowledge_graph.ts b/src/graph/knowledge_graph.ts
@@ -174,35 +174,9 @@ export default class KnowledgeGraph {
     });
 
     //handle TRAPI APIs (Situation A of https://github.com/biothings/BioThings_Explorer_TRAPI/issues/208) and APIs that define 'edge-atributes' in x-bte
-    const seenPmids = new Set();
     kgEdge.attributes['edge-attributes']?.forEach((attribute) => {
-      // Do not add multiple SemmedDB sentences/other "supporting study results" from the same publication
-      if (attribute.attribute_type_id === "biolink:has_supporting_study_result" && attribute?.attributes?.find((attr) => attr.attribute_type_id === "biolink:publications")) {
-        const publication = attribute.attributes.find((attr) => attr.attribute_type_id === "biolink:publications").value;
-        // publication has been seen or cap reached
-        if (seenPmids.has(publication) || seenPmids.size >= 50) {
-          seenPmids.add(publication);
-          return;
-        } 
-        seenPmids.add(publication);
-      }
-
       attributes.push(attribute);
     });
-
-    // update evidence count after PMIDs have been merged (for SemmedDB)
-    if (seenPmids.size != 0) {
-      const evidenceAttr = attributes.find(attr => attr.attribute_type_id === 'biolink:evidence_count');
-      if (evidenceAttr) {
-        evidenceAttr.value = seenPmids.size;
-      } else {
-        attributes.push({
-          attribute_type_id: 'biolink:evidence_count',
-          value: seenPmids.size,
-        });
-      }
-    }
-
     return attributes;
   }
 

diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts
@@ -87,7 +87,7 @@ export default class InferredQueryHandler {
     this.CREATIVE_LIMIT = process.env.CREATIVE_LIMIT ? parseInt(process.env.CREATIVE_LIMIT) : 500;
     this.CREATIVE_TIMEOUT = process.env.CREATIVE_TIMEOUT_S
       ? parseInt(process.env.CREATIVE_TIMEOUT) * 1000
-      : 4.75 * 60 * 1000;
+      : 4.50 * 60 * 1000;
   }
 
   get queryIsValid(): boolean {