Merge pull request #259 from bcgsc/feature/DEVSU-2012-add-iprEvidence…

…Level-to-kbMatches feature/DEVSU-2012-add-iprEvidenceLevel-to-kbMatches
bcgsc · Jul 5, 2023 · 5029136 · 5029136
2 parents ed1f9f5 + 9f01387
commit 5029136
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Showing 3 changed files with 38 additions and 8 deletions.
diff --git a/app/routes/report/kbMatches.js b/app/routes/report/kbMatches.js
@@ -59,7 +59,7 @@ router.route('/:kbMatch([A-z0-9-]{36})')
 
 router.route('/')
   .get(async (req, res) => {
-    const {query: {matchedCancer, approvedTherapy, category}} = req;
+    const {query: {matchedCancer, approvedTherapy, category, iprEvidenceLevel}} = req;
 
     // Check cache
     const key = generateKey(`/reports/${req.report.ident}/kb-matches`, req.query);
@@ -79,6 +79,7 @@ router.route('/')
       const results = await db.models.kbMatches.scope('public').findAll({
         where: {
           reportId: req.report.id,
+          ...((iprEvidenceLevel) ? {iprEvidenceLevel: {[Op.in]: iprEvidenceLevel.split(',')}} : {}),
           ...((category) ? {category: {[Op.in]: category.split(',')}} : {}),
           ...((typeof matchedCancer === 'boolean') ? {matchedCancer} : {}),
           ...((typeof approvedTherapy === 'boolean') ? {approvedTherapy} : {}),

diff --git a/app/routes/swagger/swagger.json b/app/routes/swagger/swagger.json
@@ -4421,16 +4421,21 @@
             }
           },
           {
-            "name": "rapidTable",
+            "name": "category",
             "in": "query",
             "required": false,
-            "description": "Filter according to chosen rapidTable",
+            "description": "Filter by category field. Comma separated field",
             "schema": {
-              "type": "string",
-              "enum": [
-                "therapeuticAssociation",
-                "cancerRelevance"
-              ]
+              "type": "string"
+            }
+          },
+          {
+            "name": "iprEvidenceLevel",
+            "in": "query",
+            "required": false,
+            "description": "Filter by iprEvidenceLevel field. Comma separated field",
+            "schema": {
+              "type": "string"
             }
           }
         ],

diff --git a/test/routes/report/kbMatches.test.js b/test/routes/report/kbMatches.test.js
@@ -46,6 +46,7 @@ describe('/reports/{REPORTID}/kb-matches', () => {
   let variant;
   let kbMatch;
   let createData;
+  let createDataFilteringTest;
 
   beforeAll(async () => {
     // Get genomic template
@@ -69,9 +70,19 @@ describe('/reports/{REPORTID}/kb-matches', () => {
       variantId: variant.id,
       category: 'unknown',
       variantType: 'cnv',
+      iprEvidenceLevel: 'IPR-A',
+    };
+
+    createDataFilteringTest = {
+      reportId: report.id,
+      variantId: variant.id,
+      category: 'unknown',
+      variantType: 'cnv',
+      iprEvidenceLevel: 'IPR-B',
     };
 
     kbMatch = await db.models.kbMatches.create(createData);
+    await db.models.kbMatches.create(createDataFilteringTest);
   }, LONGER_TIMEOUT);
 
   describe('GET', () => {
@@ -86,6 +97,19 @@ describe('/reports/{REPORTID}/kb-matches', () => {
       checkKbMatch(res.body[0]);
     });
 
+    test('Filtering kb-matches is ok', async () => {
+      const res = await request
+        .get(`/api/reports/${report.ident}/kb-matches`)
+        .query({iprEvidenceLevel: 'IPR-A,IPR-C'})
+        .auth(username, password)
+        .type('json')
+        .expect(HTTP_STATUS.OK);
+
+      expect(Array.isArray(res.body)).toBe(true);
+      checkKbMatch(res.body[0]);
+      res.body.every((match) => {return expect(match.iprEvidenceLevel).toEqual('IPR-A');});
+    });
+
     test('Getting a specific kb-match is ok', async () => {
       const res = await request
         .get(`/api/reports/${report.ident}/kb-matches/${kbMatch.ident}`)