do pfocr for creative mode at the end

biothings · Sep 16, 2024 · cbb8497 · cbb8497
1 parent 6010ce6
commit cbb8497
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Showing 3 changed files with 33 additions and 22 deletions.
diff --git a/src/index.ts b/src/index.ts
@@ -474,10 +474,10 @@ export default class TRAPIQueryHandler {
   }
 
   async _processQueryGraph(queryGraph: TrapiQueryGraph): Promise<QEdge[]> {
-const queryGraphHandler = new QueryGraph(queryGraph, this.options.schema, this._queryIsPathfinder());
-const queryEdges = await queryGraphHandler.calculateEdges();
-this.logs = [...this.logs, ...queryGraphHandler.logs];
-return queryEdges;
+    const queryGraphHandler = new QueryGraph(queryGraph, this.options.schema, this._queryIsPathfinder());
+    const queryEdges = await queryGraphHandler.calculateEdges();
+    this.logs = [...this.logs, ...queryGraphHandler.logs];
+    return queryEdges;
   }
 
   async _edgesSupported(qEdges: QEdge[], metaKG: MetaKG): Promise<boolean> {
@@ -782,7 +782,9 @@ return queryEdges;
     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();
 

diff --git a/src/inferred_mode/inferred_mode.ts b/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 {
@@ -301,7 +302,6 @@ export default class InferredQueryHandler {
           [qEdge.subject]: [{ id: result.node_bindings.creativeQuerySubject[0].id, attributes: [] }],
           [qEdge.object]: [{ id: result.node_bindings.creativeQueryObject[0].id, attributes: [] }],
         },
-        pfocr: result.pfocr?.length ? result.pfocr : undefined,
         analyses: [
           {
             resource_id: result.analyses[0].resource_id,
@@ -473,20 +473,6 @@ 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
@@ -644,7 +630,7 @@ 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);
@@ -725,6 +711,10 @@ 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
+    this.logs = [...this.logs, ...(await enrichTrapiResultsWithPfocrFigures(response, true))];
+
     // get the final summary log
     if (successfulQueries) {
       this.parent

diff --git a/src/results_assembly/pfocr.ts b/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) => {