perf: ⚡ increase the speed to generate TRAPI response

#54
biothings · Feb 14, 2021 · ea23686 · ea23686
1 parent 8c0e585
commit ea23686
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Showing 4 changed files with 58 additions and 39 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -43,7 +43,7 @@
     "@commitlint/cli": "^11.0.0",
     "@commitlint/config-conventional": "^11.0.0",
     "axios": "^0.21.1",
-    "biomedical_id_resolver": "^2.1.1",
+    "biomedical_id_resolver": "^2.2.1",
     "biothings-explorer-graphql": "2.1.1",
     "body-parser": "^1.19.0",
     "camelcase": "^6.2.0",

diff --git a/src/controllers/QueryGraphHandler/knowledge_graph.js b/src/controllers/QueryGraphHandler/knowledge_graph.js
@@ -22,33 +22,29 @@ module.exports = class KnowledgeGraph {
 
     _createInputNode(record) {
         return {
-            [helper._getInputID(record)]: {
-                category: "biolink:" + helper._getInputCategory(record),
-                name: helper._getInputLabel(record),
-                attributes: [
-                    {
-                        name: "equivalent_identifiers",
-                        value: helper._getInputEquivalentIds(record),
-                        type: "biolink:id"
-                    }
-                ]
-            }
+            category: "biolink:" + helper._getInputCategory(record),
+            name: helper._getInputLabel(record),
+            attributes: [
+                {
+                    name: "equivalent_identifiers",
+                    value: helper._getInputEquivalentIds(record),
+                    type: "biolink:id"
+                }
+            ]
         }
     }
 
     _createOutputNode(record) {
         return {
-            [helper._getOutputID(record)]: {
-                category: "biolink:" + helper._getOutputCategory(record),
-                name: helper._getOutputLabel(record),
-                attributes: [
-                    {
-                        name: "equivalent_identifiers",
-                        value: helper._getOutputEquivalentIds(record),
-                        type: "biolink:id"
-                    }
-                ]
-            }
+            category: "biolink:" + helper._getOutputCategory(record),
+            name: helper._getOutputLabel(record),
+            attributes: [
+                {
+                    name: "equivalent_identifiers",
+                    value: helper._getOutputEquivalentIds(record),
+                    type: "biolink:id"
+                }
+            ]
         }
     }
 
@@ -80,20 +76,29 @@ module.exports = class KnowledgeGraph {
 
     _createEdge(record) {
         return {
-            [helper._createUniqueEdgeID(record)]: {
-                predicate: "biolink:" + ((typeof record.$edge_metadata.trapi_qEdge_obj.getQueryPredicate() === "undefined") ? record.$edge_metadata.predicate : record.$edge_metadata.trapi_qEdge_obj.getQueryPredicate()),
-                subject: helper._getInputID(record),
-                object: helper._getOutputID(record),
-                attributes: this._createAttributes(record)
-            }
+            predicate: "biolink:" + ((typeof record.$edge_metadata.trapi_qEdge_obj.getQueryPredicate() === "undefined") ? record.$edge_metadata.predicate : record.$edge_metadata.trapi_qEdge_obj.getQueryPredicate()),
+            subject: helper._getInputID(record),
+            object: helper._getOutputID(record),
+            attributes: this._createAttributes(record)
         }
     }
 
     update(queryResult) {
         queryResult.map(record => {
-            this.nodes = { ...this.nodes, ...this._createInputNode(record) };
-            this.nodes = { ...this.nodes, ...this._createOutputNode(record) };
-            this.edges = { ...this.edges, ...this._createEdge(record) };
+            debug(`record input: ${JSON.stringify(record.$input)}`);
+            debug(`record output: ${JSON.stringify(record.$output)}`);
+            if (!(helper._getInputID(record) in this.nodes)) {
+                this.nodes[helper._getInputID(record)] = this._createInputNode(record);
+            }
+            if (!(helper._getOutputID(record) in this.nodes)) {
+                this.nodes[helper._getOutputID(record)] = this._createOutputNode(record);
+            }
+            if (!(helper._createUniqueEdgeID(record) in this.edges)) {
+                this.edges[helper._createUniqueEdgeID(record)] = this._createEdge(record);
+            }
+            // this.nodes = { ...this.nodes, ...this._createInputNode(record) };
+            // this.nodes = { ...this.nodes, ...this._createOutputNode(record) };
+            // this.edges = { ...this.edges, ...this._createEdge(record) };
 
         })
         this.kg = {

diff --git a/src/controllers/QueryGraphHandler/update_nodes.js b/src/controllers/QueryGraphHandler/update_nodes.js
@@ -1,5 +1,4 @@
 const id_resolver = require("biomedical_id_resolver");
-const GraphHelper = require("./helper");
 const _ = require("lodash");
 const debug = require("debug")("biothings-explorer-trapi:nodeUpdateHandler");
 
@@ -77,10 +76,25 @@ module.exports = class NodesUpdateHandler {
      * @param {object} queryResult - query response
      */
     update(queryResult) {
+        const node_dict = {};
+        const id_dict = {};
+        // queryResult.map(record => {
+        //     record.$edge_metadata.trapi_qEdge_obj.getOutputNode().updateEquivalentIDs(
+        //         this._createEquivalentIDsObject(record)
+        //     );
+        // })
         queryResult.map(record => {
-            record.$edge_metadata.trapi_qEdge_obj.getOutputNode().updateEquivalentIDs(
-                this._createEquivalentIDsObject(record)
-            );
+            const nodeID = record.$edge_metadata.trapi_qEdge_obj.getOutputNode().getID();
+            if (!(nodeID in id_dict)) {
+                id_dict[nodeID] = {};
+                node_dict[nodeID] = record.$edge_metadata.trapi_qEdge_obj.getOutputNode();
+            }
+            if (!(record.$output.obj.primaryID in id_dict[nodeID])) {
+                id_dict[nodeID][record.$output.obj.primaryID] = record.$output.obj;
+            }
         })
+        for (const nodeID in id_dict) {
+            node_dict[nodeID].updateEquivalentIDs(id_dict[nodeID]);
+        }
     }
 }