get missing categories using sri resolver prior to query process

biothings · Sep 7, 2021 · 2378ec5 · 2378ec5
1 parent 32fc883
commit 2378ec5
Show file tree

Hide file tree

Showing 2 changed files with 57 additions and 12 deletions.
diff --git a/src/index.js b/src/index.js
@@ -81,10 +81,10 @@ exports.TRAPIQueryHandler = class TRAPIQueryHandler {
    * @private
    * @param {object} queryGraph - TRAPI Query Graph Object
    */
-   _processQueryGraph_2(queryGraph) {
+   async _processQueryGraph_2(queryGraph) {
     try {
       let queryGraphHandler = new QueryGraph(queryGraph);
-      let res = queryGraphHandler.calculateEdges();
+      let res = await queryGraphHandler.calculateEdges();
       this.logs = [...this.logs, ...queryGraphHandler.logs];
       return res;
     } catch (err) {
@@ -141,7 +141,7 @@ exports.TRAPIQueryHandler = class TRAPIQueryHandler {
     debug('Start to load metakg.');
     const kg = this._loadMetaKG(this.smartapiID, this.team);
     debug('MetaKG successfully loaded!');
-    let queryEdges = this._processQueryGraph_2(this.queryGraph);
+    let queryEdges = await this._processQueryGraph_2(this.queryGraph);
     debug(`(3) All edges created ${JSON.stringify(queryEdges)}`);
     const manager = new EdgeManager(queryEdges);
     while (manager.getEdgesNotExecuted()) {

diff --git a/src/query_graph.js b/src/query_graph.js
@@ -1,13 +1,13 @@
 const QNode = require('./query_node');
 const QEdge = require('./query_edge');
 const QExecEdge = require('./query_execution_edge');
-const _ = require('lodash');
 const InvalidQueryGraphError = require('./exceptions/invalid_query_graph_error');
 const LogEntry = require('./log_entry');
 const NewExeEdge = require('./query_execution_edge_2');
 const MAX_DEPTH = 3;
 const debug = require('debug')('bte:biothings-explorer-trapi:query_graph');
 const QNode2 = require('./query_node_2');
+const id_resolver = require('biomedical_id_resolver');
 
 module.exports = class QueryGraphHandler {
   constructor(queryGraph) {
@@ -58,13 +58,57 @@ module.exports = class QueryGraphHandler {
     return nodes;
   }
 
+  /**
+   * @private
+   */
+    async _findNodeCategories(ids) {
+      if (ids.length == 1) {
+        let category = await id_resolver.resolveSRI({
+            unknown: ids
+        });
+        debug(`Query node missing categories...Looking for match...`);
+        if (Object.hasOwnProperty.call(category, ids[0])) {
+            category = category[ids[0]][0]['semanticType'];
+            return ["biolink:" + category];
+        }else{
+            debug(`No category match found for ${JSON.stringify(ids)}.`);
+            return [];
+        }
+    }else{
+      debug(`(Error) Can't find category matches of multiple IDs.`);
+      return [];
+    }
+  }
+
    /**
    * @private
    */
-    _storeNodes_2() {
+    async _storeNodes_2() {
       let nodes = {};
       for (let node_id in this.queryGraph.nodes) {
-        nodes[node_id] = new QNode2(node_id, this.queryGraph.nodes[node_id]);
+        //if node has ID but no categories
+        if (
+          (!Object.hasOwnProperty.call(this.queryGraph.nodes[node_id], 'categories') &&
+          Object.hasOwnProperty.call(this.queryGraph.nodes[node_id], 'ids')) ||
+          (Object.hasOwnProperty.call(this.queryGraph.nodes[node_id], 'categories') &&
+          this.queryGraph.nodes[node_id].categories.length == 0 &&
+          Object.hasOwnProperty.call(this.queryGraph.nodes[node_id], 'ids'))
+          ) {
+          let category = await this._findNodeCategories(this.queryGraph.nodes[node_id].ids);
+          this.queryGraph.nodes[node_id].categories = category;
+          debug(`Node category found. Assigning value: ${JSON.stringify(this.queryGraph.nodes[node_id])}`);
+          this.logs.push(
+            new LogEntry(
+            'DEBUG',
+            null, 
+            `Assigned missing node ID category: ${JSON.stringify(this.queryGraph.nodes[node_id])}`).getLog(),
+          );
+          nodes[node_id] = new QNode2(node_id, this.queryGraph.nodes[node_id]);
+        }else{
+          debug(`Creating node...`);
+          nodes[node_id] = new QNode2(node_id, this.queryGraph.nodes[node_id]);
+        }
+
       }
       this.logs.push(
         new LogEntry('DEBUG', null, `BTE identified ${Object.keys(nodes).length} QNodes from your query graph`).getLog(),
@@ -75,9 +119,9 @@ module.exports = class QueryGraphHandler {
   /**
    * @private
    */
-  _storeEdges() {
+  async _storeEdges() {
     if (this.nodes === undefined) {
-      this.nodes = this._storeNodes();
+      this.nodes = await this._storeNodes();
     }
     let edges = {};
     for (let edge_id in this.queryGraph.edges) {
@@ -99,9 +143,9 @@ module.exports = class QueryGraphHandler {
   /**
    * @private
    */
-   _storeEdges_2() {
+   async _storeEdges_2() {
     if (this.nodes === undefined) {
-      this.nodes = this._storeNodes_2();
+      this.nodes = await this._storeNodes_2();
     }
     let edges = {};
     for (let edge_id in this.queryGraph.edges) {
@@ -158,11 +202,12 @@ module.exports = class QueryGraphHandler {
   /**
    *
    */
-  calculateEdges() {
+  async calculateEdges() {
+    this._validate(this.queryGraph);
     //populate edge and node info
     debug(`(1) Creating edges for manager...`);
     if (this.edges === undefined) {
-      this.edges = this._storeEdges_2();
+      this.edges = await this._storeEdges_2();
     }
     let edges = {};
     let edge_index = 0;