Merge pull request #219 from biothings/semmed-sentences

properly merge semmedb sentences

src/graph/kg_edge.ts

@@ -120,7 +120,8 @@ export default class KGEdge {
   addAdditionalAttributes(name: string, value: string | string[] | TrapiAttribute[]): void {
     // special handling for full edge attributes
     if (name === 'edge-attributes') {
-      this.attributes[name] = value as TrapiAttribute[];
+      if (this.attributes[name]) this.attributes[name] = [...this.attributes[name], ...value as TrapiAttribute[]];
+      else this.attributes[name] = value as TrapiAttribute[];
       return;
     }
 

src/graph/knowledge_graph.ts

@@ -166,9 +166,35 @@ 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;
   }