Merge pull request #125 from biothings/property-warning

Check Qnode/Qedge properties
biothings · Jan 6, 2023 · e65e2a2 · e65e2a2
2 parents 98d9f10 + ab76c46
commit e65e2a2
Show file tree

Hide file tree

Showing 4 changed files with 60 additions and 6 deletions.
diff --git a/__test__/integration/integrity.test.js b/__test__/integration/integrity.test.js
@@ -25,7 +25,7 @@ describe('Testing TRAPIQueryHandler Module', () => {
     queryHandler.setQueryGraph(query.message.query_graph);
     await queryHandler.query();
     const res = queryHandler.getResponse();
-    console.log(res);
+    // console.log(res);
     expect(res.message.knowledge_graph.nodes).toHaveProperty('NCBIGene:111');
   });
 

diff --git a/src/index.js b/src/index.js
@@ -88,13 +88,13 @@ exports.TRAPIQueryHandler = class TRAPIQueryHandler {
         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;
@@ -120,7 +120,7 @@ exports.TRAPIQueryHandler = class TRAPIQueryHandler {
    */
   async _processQueryGraph(queryGraph) {
     try {
-      let queryGraphHandler = new QueryGraph(queryGraph);
+      let queryGraphHandler = new QueryGraph(queryGraph, this.options.schema);
       let queryEdges = await queryGraphHandler.calculateEdges();
       this.logs = [...this.logs, ...queryGraphHandler.logs];
       return queryEdges;

diff --git a/src/query_graph.js b/src/query_graph.js
@@ -9,8 +9,9 @@ const _ = require('lodash');
 const utils = require('./utils');
 
 module.exports = class QueryGraphHandler {
-  constructor(queryGraph) {
+  constructor(queryGraph, schema) {
     this.queryGraph = queryGraph;
+    this.schema = schema;
     this.logs = [];
   }
 
@@ -93,6 +94,56 @@ module.exports = class QueryGraphHandler {
     }
   }
 
+  _validateNodeProperties(queryGraph) {
+    const schemProps = this.schema?.components?.schemas?.QNode?.properties ? this.schema.components.schemas.QNode.properties : {};
+    const nodeProperties = new Set(Object.keys(schemProps));
+    const badProperties = new Set();
+    const badNodes = new Set();
+    for (const nodeID in queryGraph.nodes) {
+      for (const property in queryGraph.nodes[nodeID]) {
+        if (!nodeProperties.has(property)) {
+          badProperties.add(property);
+          badNodes.add(nodeID);
+        }
+      }
+    }
+
+    if (badProperties.size !== 0) {
+      this.logs.push(
+        new LogEntry(
+          'WARNING',
+          null,
+          `Ignoring unrecognized properties (${[...badProperties].join(',')}) on nodes (${[...badNodes].join(',')}).`,
+        ).getLog()
+      );
+    }
+  }
+
+  _validateEdgeProperties(queryGraph) {
+    const schemProps = this.schema?.components?.schemas?.QEdge?.properties ? this.schema.components.schemas.QEdge.properties : {};
+    const edgeProperties = new Set(Object.keys(schemProps));
+    const badProperties = new Set();
+    const badEdges = new Set();
+    for (const edgeID in queryGraph.edges) {
+      for (const property in queryGraph.edges[edgeID]) {
+        if (!edgeProperties.has(property)) {
+          badProperties.add(property);
+          badEdges.add(edgeID);
+        }
+      }
+    }
+
+    if (badProperties.size !== 0) {
+      this.logs.push(
+        new LogEntry(
+          'WARNING',
+          null,
+          `Ignoring unrecognized properties (${[...badProperties].join(',')}) on edges (${[...badEdges].join(',')}).`,
+        ).getLog()
+      );
+    }
+  }
+
   _validateNoDuplicateQualifierTypes(queryGraph) {
     Object.entries(queryGraph.edges).forEach(([id, edge]) => {
       if (edge.qualifier_constraints) {
@@ -117,6 +168,8 @@ module.exports = class QueryGraphHandler {
     this._validateOneNodeID(queryGraph);
     this._validateNodeEdgeCorrespondence(queryGraph);
     this._validateDuplicateEdges(queryGraph);
+    this._validateNodeProperties(queryGraph);
+    this._validateEdgeProperties(queryGraph);
     this._validateCycles(queryGraph);
     this._validateNoDuplicateQualifierTypes(queryGraph);
   }

diff --git a/tsconfig.json b/tsconfig.json
@@ -11,7 +11,8 @@
         "esModuleInterop": true,
         "resolveJsonModule": true,
         "strict": false,
-        "noImplicitAny": false
+        "noImplicitAny": false,
+        "skipLibCheck": true
     },
     "include": [
         "./src/**/*",