Fix tests

biothings · Oct 7, 2022 · 7016e3e · 7016e3e
1 parent 3edd604
commit 7016e3e
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Showing 5 changed files with 10 additions and 8 deletions.
diff --git a/__test__/integration/TRAPIGeneralizedQuery.test.js b/__test__/integration/TRAPIGeneralizedQuery.test.js
@@ -26,7 +26,7 @@ describe("Testing TRAPI QueryHandler Generalized Query Handling", () => {
 
     describe("Testing query function", () => {
         test.skip("One hop has only nodes specified", async (done) => {
-            const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler();
+            const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler({});
             queryHandler.setQueryGraph(OneHopQuery);
             await queryHandler.query();
             let res = queryHandler.getResponse();

diff --git a/__test__/integration/TRAPIQueryHandler.test.js b/__test__/integration/TRAPIQueryHandler.test.js
@@ -22,7 +22,7 @@ describe("Testing TRAPIQueryHandler Module", () => {
     };
     describe("Testing query function", () => {
         test("test with one query edge", async () => {
-            const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler();
+            const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler({});
             queryHandler.setQueryGraph(OneHopQuery);
             await queryHandler.query();
             expect(queryHandler.knowledgeGraph.kg).toHaveProperty('nodes');

diff --git a/__test__/integration/integrity.test.js b/__test__/integration/integrity.test.js
@@ -8,7 +8,7 @@ describe("Testing TRAPIQueryHandler Module", () => {
     //skip until we figure out why it returns no results
     //https://suwulab.slack.com/archives/CC218TEKC/p1624558136437200
     test.skip("When looking for chemicals affected by Phenotype Increased Urinary Glycerol, Glycerol should pop up", async () => {
-        const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler({}, undefined, undefined, true);
+        const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler({}, {}, undefined, undefined, true);
         const query = JSON.parse(fs.readFileSync(path.join(example_foler, 'increased_urinary_glycerol_affects_glycerol.json')));
         queryHandler.setQueryGraph(query.message.query_graph);
         await queryHandler.query();
@@ -17,7 +17,7 @@ describe("Testing TRAPIQueryHandler Module", () => {
     })
 
     test("When looking for genes related to Disease DYSKINESIA, FAMILIAL, WITH FACIAL MYOKYMIA, ACDY5 should pop up", async () => {
-        const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler({}, undefined, undefined, true);
+        const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler({}, {}, undefined, undefined, true);
         const query = JSON.parse(fs.readFileSync(path.join(example_foler, 'FDFM_caused_by_ACDY5.json')));
         queryHandler.setQueryGraph(query.message.query_graph);
         await queryHandler.query();
@@ -27,7 +27,7 @@ describe("Testing TRAPIQueryHandler Module", () => {
 
     //skip this test for now as the test query needs to be re-evaluated and the value of 'CHEBI:3962' needs to be updated.
     test.skip("When looking for chemicals targeting IL1 Signaling patway, curcumin should pop up", async () => {
-        const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler({}, undefined, undefined, true);
+        const queryHandler = new TRAPIQueryHandler.TRAPIQueryHandler({}, {}, undefined, undefined, true);
         const query = JSON.parse(fs.readFileSync(path.join(example_foler, 'chemicals_targeting_IL1_Signaling_Pathway.json')));
         queryHandler.setQueryGraph(query.message.query_graph);
         await queryHandler.query();

diff --git a/src/inferred_mode/inferred_mode.js b/src/inferred_mode/inferred_mode.js
@@ -178,7 +178,7 @@ module.exports = async (parent, TRAPIQueryHandler, queryGraph, logs, options, pa
       if (stop) {
         return;
       }
-      const handler = new TRAPIQueryHandler(options, path, predicatePath, includeReasoner);
+      const handler = new TRAPIQueryHandler({}, options, path, predicatePath, includeReasoner);
       handler.setQueryGraph(queryGraph);
       try {
         await handler.query();

diff --git a/src/query_graph.js b/src/query_graph.js
@@ -85,7 +85,8 @@ module.exports = class QueryGraphHandler {
   }
 
   _validateNodeProperties(queryGraph) {
-    const nodeProperties = new Set(Object.keys(this.schema.components.schemas.QNode.properties));
+    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();
     for (const nodeID in queryGraph.nodes) {
       for (const property in queryGraph.nodes[nodeID]) {
@@ -107,7 +108,8 @@ module.exports = class QueryGraphHandler {
   }
 
   _validateEdgeProperties(queryGraph) {
-    const edgeProperties = new Set(Object.keys(this.schema.components.schemas.QEdge.properties));
+    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();
     for (const edgeID in queryGraph.edges) {
       for (const property in queryGraph.edges[edgeID]) {