Merge pull request #188 from biothings/empty-attributes

Add empty attributes property to node/edge bindings and aux-graphs

Author: tokebe

src/index.ts

@@ -211,7 +211,7 @@ export default class TRAPIQueryHandler {
         suffix += 1;
       }
       const supportGraphID = `support${suffix}-${boundEdgeID}`;
-      auxGraphs[supportGraphID] = { edges: supportGraph };
+      auxGraphs[supportGraphID] = { edges: supportGraph, attributes: [] };
       if (!edgesIDsByAuxGraphID[supportGraphID]) {
         edgesIDsByAuxGraphID[supportGraphID] = new Set();
       }
@@ -254,7 +254,7 @@ export default class TRAPIQueryHandler {
                     boundIDs.add(binding.id);
                   }
                 } else if (!boundIDs.has(nodesToRebind[binding.id].newNode)) {
-                  newBindings.push({ id: nodesToRebind[binding.id].newNode });
+                  newBindings.push({ id: nodesToRebind[binding.id].newNode, attributes: [] });
                   boundIDs.add(nodesToRebind[binding.id].newNode);
                 }
                 return { boundIDs, newBindings };
@@ -276,7 +276,7 @@ export default class TRAPIQueryHandler {
                     boundIDs.add(binding.id);
                   }
                 } else if (!boundIDs.has(edgesToRebind[binding.id])) {
-                  newBindings.push({ id: edgesToRebind[binding.id] });
+                  newBindings.push({ id: edgesToRebind[binding.id], attributes: [] });
                   boundIDs.add(edgesToRebind[binding.id]);
                   resultBoundEdgesWithAuxGraphs.add(edgesToRebind[binding.id]);
                 }

src/inferred_mode/inferred_mode.ts

@@ -288,8 +288,8 @@ export default class InferredQueryHandler {
     newResponse.message.results.forEach((result) => {
       const translatedResult: TrapiResult = {
         node_bindings: {
-          [qEdge.subject]: [{ id: result.node_bindings.creativeQuerySubject[0].id }],
-          [qEdge.object]: [{ id: result.node_bindings.creativeQueryObject[0].id }],
+          [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: [
@@ -311,14 +311,14 @@ export default class InferredQueryHandler {
       // Direct edge answers stand on their own, not as an inferred edge.
       if (Object.keys(result.node_bindings).length == 2) {
         const boundEdgeID = Object.values(result.analyses[0].edge_bindings)[0][0].id;
-        translatedResult.analyses[0].edge_bindings = { [qEdgeID]: [{ id: boundEdgeID }] };
+        translatedResult.analyses[0].edge_bindings = { [qEdgeID]: [{ id: boundEdgeID, attributes: [] }] };
       } else {
         // Create an aux graph using the result and associate it with an inferred Edge
         const inferredEdgeID = `inferred-${resultCreativeSubjectID}-${qEdge.predicates[0].replace(
           'biolink:',
           '',
         )}-${resultCreativeObjectID}`;
-        translatedResult.analyses[0].edge_bindings = { [qEdgeID]: [{ id: inferredEdgeID }] };
+        translatedResult.analyses[0].edge_bindings = { [qEdgeID]: [{ id: inferredEdgeID, attributes: [] }] };
         if (!combinedResponse.message.knowledge_graph.edges[inferredEdgeID]) {
           combinedResponse.message.knowledge_graph.edges[inferredEdgeID] = {
             subject: resultCreativeSubjectID,
@@ -357,6 +357,7 @@ export default class InferredQueryHandler {
             },
             [] as string[],
           ),
+          attributes: []
         };
       }
 

src/results_assembly/query_results.ts

@@ -452,18 +452,21 @@ export default class TrapiResultsAssembler {
             result.node_bindings[inputQNodeID] = Array.from(inputPrimaryCuries).map((inputPrimaryCurie) => {
               return {
                 id: inputPrimaryCurie,
+                attributes: [],
               };
             });
 
             result.node_bindings[outputQNodeID] = Array.from(outputPrimaryCuries).map((outputPrimaryCurie) => {
               return {
                 id: outputPrimaryCurie,
+                attributes: [],
               };
             });
 
             result.analyses[0].edge_bindings[qEdgeID] = Array.from(recordHashes).map((recordHash) => {
               return {
                 id: recordHash,
+                attributes: [],
               };
             });
           },