Merge pull request #113 from biothings/node-expansion

feat: perform node expansion
biothings · Jan 4, 2023 · 98d9f10 · 98d9f10
2 parents add1e58 + 85d434a
commit 98d9f10
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Showing 7 changed files with 28 additions and 112 deletions.
diff --git a/data/templateGroups.json b/data/templateGroups.json
@@ -9,10 +9,9 @@
                "DiseaseOrPhenotypicFeature"
               ],
     "templates": [
-      "Chem-subclassDoP-DoP.json",
-      "m1-Chem-Pheno-DoP.json",
+      "Chem-DoP.json",
       "m4-Chem-Gene-DoP.json",
-      "m7-Chem-Pheno-subclassDoP-DoP.json"
+      "m1-Chem-Pheno-DoP.json"
     ]
   }
 ]
diff --git a/...lates/less-promising/straightforward.json → ...mplates/Drug-treats-Disease/Chem-DoP.json b/...lates/less-promising/straightforward.json → ...mplates/Drug-treats-Disease/Chem-DoP.json
@@ -6,7 +6,7 @@
                     "categories":["biolink:ChemicalEntity"]
                 },
                 "creativeQueryObject": {
-                    "categories":["biolink:Disease"]
+                    "categories":["biolink:DiseaseOrPhenotypicFeature"]
                }
             },
             "edges": {

diff --git a/data/templates/Drug-treats-Disease/Chem-subclassDoP-DoP.json b/data/templates/Drug-treats-Disease/Chem-subclassDoP-DoP.json
diff --git a/data/templates/Drug-treats-Disease/m7-Chem-Pheno-subclassDoP-DoP.json b/data/templates/Drug-treats-Disease/m7-Chem-Pheno-subclassDoP-DoP.json
diff --git a/data/templates/less-promising/m2-Disease-subclassDoP-Gene-Chem.json b/data/templates/less-promising/m2-Disease-subclassDoP-Gene-Chem.json
diff --git a/package.json b/package.json
@@ -45,6 +45,7 @@
   },
   "dependencies": {
     "@biothings-explorer/call-apis": "^1.24.0",
+    "@biothings-explorer/node-expansion": "^1.0.0",
     "@biothings-explorer/smartapi-kg": "^4.0.0",
     "async": "^3.2.1",
     "biolink-model": "^0.4.0",

diff --git a/src/index.js b/src/index.js
@@ -14,6 +14,7 @@ const LogEntry = require('./log_entry');
 const { redisClient } = require('./redis-client');
 const config = require('./config');
 const fs = require('fs').promises;
+const { getDescendants } = require('@biothings-explorer/node-expansion');
 const { getTemplates, supportedLookups } = require('./inferred_mode/template_lookup');
 const handleInferredMode = require('./inferred_mode/inferred_mode');
 const id_resolver = require('biomedical_id_resolver');
@@ -81,6 +82,29 @@ exports.TRAPIQueryHandler = class TRAPIQueryHandler {
    */
   setQueryGraph(queryGraph) {
     this.queryGraph = queryGraph;
+    for (const nodeId in queryGraph.nodes) {
+      // perform node expansion
+      if (queryGraph.nodes[nodeId].ids && !this._queryUsesInferredMode()) {
+        let expanded = Object.values(getDescendants(queryGraph.nodes[nodeId].ids)).flat();
+        console.log(expanded.length);
+        expanded = _.uniq([...queryGraph.nodes[nodeId].ids, ...expanded]);
+
+        let log_msg = `Expanded ids for node ${nodeId}: (${queryGraph.nodes[nodeId].ids.length} ids -> ${expanded.length} ids)`;
+        debug(log_msg);
+        this.logs.push(new LogEntry('INFO', null, log_msg).getLog());
+
+        queryGraph.nodes[nodeId].ids = expanded;
+
+        //make sure is_set is true
+        if (!queryGraph.nodes[nodeId].hasOwnProperty('is_set') || !queryGraph.nodes[nodeId].is_set) {
+          queryGraph.nodes[nodeId].is_set = true;
+          log_msg = `Added is_set:true to node ${nodeId}`;
+          debug(log_msg);
+          this.logs.push(new LogEntry('INFO', null, log_msg).getLog());
+        }
+
+      }
+    }
   }
 
   _initializeResponse() {