Merge pull request #260 from bcgsc/release/v7.16.2

Release/v7.16.2

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} : {}),

app/routes/report/report.js

@@ -6,10 +6,8 @@ const createReport = require('../../libs/createReport');
 const {parseReportSortQuery} = require('../../libs/queryOperations');
 const db = require('../../models');
 const logger = require('../../log');
-const cache = require('../../cache');
 const {getUserProjects} = require('../../libs/helperFunctions');
 
-const {generateKey} = require('../../libs/cacheFunctions');
 const {hasAccessToNonProdReports} = require('../../libs/helperFunctions');
 
 const reportMiddleware = require('../../middleware/report');
@@ -158,19 +156,6 @@ router.route('/')
       }
     }
 
-    // Generate cache key
-    const key = (req.query.role) ? null : generateKey('/reports', req.query, {projectAccess: projects});
-
-    try {
-      const cacheResults = await cache.get(key);
-      if (cacheResults) {
-        res.type('json');
-        return res.send(cacheResults);
-      }
-    } catch (error) {
-      logger.error(`Error while checking cache for reports ${error}`);
-    }
-
     // Generate options for report query
     const opts = {
       where: {
@@ -252,10 +237,6 @@ router.route('/')
       const reports = await db.models.report.scope('public').findAndCountAll(opts);
       const results = {total: reports.count, reports: reports.rows};
 
-      if (key) {
-        cache.set(key, JSON.stringify(results), 'EX', 14400);
-      }
-
       return res.json(results);
     } catch (error) {
       logger.error(`Unable to lookup reports ${error}`);

app/routes/report/variants.js

@@ -10,7 +10,7 @@ const logger = require('../../log');
 const {KB_PIVOT_MAPPING} = require('../../constants');
 
 const KBMATCHEXCLUDE = ['id', 'reportId', 'variantId', 'deletedAt', 'updatedBy'];
-const MUTATION_REGEX = '^([^\\s]+)(\\s)mutation[s]?$';
+const MUTATION_REGEX = '^([^\\s]+)(\\s)(mutation[s]?)?(missense)?$';
 
 const getVariants = async (tableName, variantType, reportId) => {
   return db.models[tableName].scope('extended').findAll({

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"
             }
           }
         ],

package.json

@@ -1,7 +1,7 @@
 {
   "private": true,
   "name": "ipr-api",
-  "version": "7.16.1",
+  "version": "7.16.2",
   "description": "Integrated Pipeline Reports API",
   "main": "bin/server.js",
   "scripts": {

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}`)

test/routes/report/variants.test.js

@@ -367,7 +367,7 @@ describe('/reports/{REPORTID}/kb-matches', () => {
       category: 'therapeutic',
       variantType: 'mut',
       iprEvidenceLevel: 'IPR-A',
-      kbVariant: 'geneX mutation',
+      kbVariant: 'geneX missense',
       matchedCancer: true,
     };