Reapply "Merge branch 'creative-pfocr-fix' of https://github.com/biot…

…hings/bte_trapi_query_graph_handler into dev"

This reverts commit 1f1a8ba.

src/index.ts

@@ -782,7 +782,9 @@ export default class TRAPIQueryHandler {
     this.bteGraph.notify();
 
     // Attempt to enrich results with PFOCR figures
-    this.logs = [...this.logs, ...(await enrichTrapiResultsWithPfocrFigures(this.getResponse()))];
+    if (!this.options.skipPfocr) {
+      this.logs = [...this.logs, ...(await enrichTrapiResultsWithPfocrFigures(this.getResponse()))];
+    }
 
     span3?.finish();
 

src/inferred_mode/inferred_mode.ts

@@ -20,6 +20,7 @@ import {
   TrapiAnalysis,
 } from '@biothings-explorer/types';
 import { CompactQualifiers } from '../index';
+import { enrichTrapiResultsWithPfocrFigures } from '../results_assembly/pfocr';
 const debug = Debug('bte:biothings-explorer-trapi:inferred-mode');
 
 export interface CombinedResponse {
@@ -311,7 +312,6 @@ export default class InferredQueryHandler {
           [qEdge.subject]: [subjectBinding],
           [qEdge.object]: [objectBinding],
         },
-        pfocr: result.pfocr?.length ? result.pfocr : undefined,
         analyses: [
           {
             resource_id: result.analyses[0].resource_id,
@@ -483,20 +483,6 @@ export default class InferredQueryHandler {
           });
         });
 
-        // Combine, re-sort, and truncate to 20 any pfocr figures
-        if (combinedResponse.message.results[resultID].pfocr || translatedResult.pfocr) {
-          let reSort = false;
-          if (combinedResponse.message.results[resultID].pfocr && translatedResult.pfocr) reSort = true;
-          let newFigures = [
-            ...(combinedResponse.message.results[resultID].pfocr ?? []),
-            ...(translatedResult.pfocr ?? []),
-          ];
-          if (reSort) {
-            newFigures = newFigures.sort((figA, figB) => figB.score - figA.score).slice(0, 20);
-          }
-          combinedResponse.message.results[resultID].pfocr = newFigures;
-        }
-
         const resScore = translatedResult.analyses[0].score;
         if (typeof combinedResponse.message.results[resultID].analyses[0].score !== 'undefined') {
           combinedResponse.message.results[resultID].analyses[0].score = resScore
@@ -654,7 +640,7 @@ export default class InferredQueryHandler {
       }
       if (global.queryInformation != null) global.queryInformation.totalRecords = 0; // Reset between templates
 
-      const handler = new TRAPIQueryHandler(this.options, this.path, this.predicatePath, this.includeReasoner);
+      const handler = new TRAPIQueryHandler({ ...this.options, skipPfocr: true }, this.path, this.predicatePath, this.includeReasoner);
       try {
         // make query and combine results/kg/logs/etc
         handler.setQueryGraph(queryGraph);
@@ -735,6 +721,12 @@ export default class InferredQueryHandler {
     response.message.results = response.message.results.slice(0, this.CREATIVE_LIMIT);
     response.description = `Query processed successfully, retrieved ${response.message.results.length} results.`;
     this.pruneKnowledgeGraph(response);
+
+    // add pfocr figures
+    if (!this.pathfinder) {
+      this.logs = [...this.logs, ...(await enrichTrapiResultsWithPfocrFigures(response, true))];
+    }
+
     // get the final summary log
     if (successfulQueries) {
       this.parent

src/inferred_mode/pathfinder.ts

@@ -16,6 +16,7 @@ import Debug from 'debug';
 import generateTemplates from './pf_template_generator';
 import biolink from '../biolink';
 import { removeBioLinkPrefix } from '../utils';
+import { enrichTrapiResultsWithPfocrFigures } from '../results_assembly/pfocr';
 const debug = Debug('bte:biothings-explorer-trapi:pathfinder');
 
 interface ResultAuxObject {
@@ -142,6 +143,9 @@ export default class PathfinderQueryHandler {
     this.parse(creativeResponse);
     this._pruneKg(creativeResponse);
 
+    // pfocr
+    this.logs = [...this.logs, ...(await enrichTrapiResultsWithPfocrFigures(creativeResponse, true))];
+
     // logs
     creativeResponse.logs = this.logs.map((log) => log.toJSON());
 

src/results_assembly/pfocr.ts

@@ -176,7 +176,7 @@ function traverseResultForNodes(result: TrapiResult, response: TrapiResponse): S
  * t: trapiResults.length
  * f: figures.length
  */
-export async function enrichTrapiResultsWithPfocrFigures(response: TrapiResponse): Promise<StampedLog[]> {
+export async function enrichTrapiResultsWithPfocrFigures(response: TrapiResponse, checkAuxGraphs = false): Promise<StampedLog[]> {
   // NOTE: This function operates on the actual TRAPI information that will be returned
   // to the client. Don't mutate what shouldn't be mutated!
   const results = response.message.results;
@@ -192,6 +192,25 @@ export async function enrichTrapiResultsWithPfocrFigures(response: TrapiResponse
     Object.values(result.node_bindings).forEach((bindings) =>
       bindings.forEach((binding) => nodes.add(response.message.knowledge_graph.nodes[binding.id])),
     );
+    // check aux graphs if applicable
+    if (checkAuxGraphs) {
+      for (const edgeId in result.analyses[0].edge_bindings) {
+        for (const eb of result.analyses[0].edge_bindings[edgeId]) {
+          const edge = response.message.knowledge_graph.edges[eb.id];
+          const supportGraphs = edge.attributes.find((attribute) => attribute.attribute_type_id == 'biolink:support_graphs');
+          if (supportGraphs) {
+            (supportGraphs.value as string[]).forEach((auxGraphID) =>
+              response.message.auxiliary_graphs[auxGraphID].edges.forEach((edgeID) => {
+                const edge = response.message.knowledge_graph.edges[edgeID];
+                nodes.add(response.message.knowledge_graph.nodes[edge.subject]);
+                nodes.add(response.message.knowledge_graph.nodes[edge.object]);
+              }),
+            );
+          }
+        }
+      }
+    }
+
     const combo: Set<string> = new Set();
     let matchedNodes = 0;
     [...nodes].forEach((node) => {