Merge branch 'develop' into feature/DEVSU-2430-notification-fail-email

bcgsc · Dec 19, 2024 · 043a091 · 043a091
2 parents 6cb0725 + 23a8c24
commit 043a091
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Showing 10 changed files with 87 additions and 112 deletions.
diff --git a/app/api/graphkb.js b/app/api/graphkb.js
@@ -90,6 +90,7 @@ const graphkbEvidenceLevels = async (graphkbToken) => {
         filters: {name: 'ipr'},
       },
     },
+    orderBy: 'displayName',
     limit: 100,
     skip: 0,
     target: 'EvidenceLevel',

diff --git a/app/models/reports/kbMatches.js b/app/models/reports/kbMatches.js
@@ -46,6 +46,9 @@ module.exports = (sequelize, Sq) => {
           return {model: sequelize.models[modelName].scope('public'), as: modelName};
         }),
       },
+      minimal: {
+        attributes: {exclude: ['id', 'reportId', 'variantId', 'deletedAt', 'updatedBy']},
+      },
       extended: {
         attributes: {exclude: ['id', 'reportId', 'variantId', 'deletedAt', 'updatedBy']},
         include: Object.values(KB_PIVOT_MAPPING).map((modelName) => {

diff --git a/app/routes/germlineSmallMutation/reports.js b/app/routes/germlineSmallMutation/reports.js
@@ -11,9 +11,6 @@ const {GERMLINE_EXCLUDE} = require('../../schemas/exclude');
 
 const db = require('../../models');
 const logger = require('../../log');
-const cache = require('../../cache');
-
-const {generateKey} = require('../../libs/cacheFunctions');
 
 const Variants = require('./util/variants');
 const gsmMiddleware = require('../../middleware/germlineSmallMutation/reports');
@@ -95,19 +92,6 @@ router.route('/')
       return group.name.trim().toLowerCase() === 'projects';
     });
 
-    // Generate cache key
-    const key = generateKey('/germline', req.query, {inProjectsGroup});
-
-    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 germline reports ${error}`);
-    }
-
     // Setup query options
     const opts = {
       where: {
@@ -160,10 +144,6 @@ router.route('/')
       const gsmReports = await db.models.germlineSmallMutation.scope('public').findAndCountAll(opts);
       const results = {total: gsmReports.count, reports: gsmReports.rows};
 
-      if (key) {
-        cache.set(key, JSON.stringify(results), 'EX', 14400);
-      }
-
       return res.json(results);
     } catch (error) {
       logger.error(`There was an error while finding all germline reports ${error}`);

diff --git a/app/routes/germlineSmallMutation/reviews.js b/app/routes/germlineSmallMutation/reviews.js
@@ -5,7 +5,6 @@ const router = express.Router({mergeParams: true});
 
 const logger = require('../../log');
 const db = require('../../models');
-const cache = require('../../cache');
 
 const schemaGenerator = require('../../schemas/schemaGenerator');
 const validateAgainstSchema = require('../../libs/validateAgainstSchema');
@@ -106,28 +105,11 @@ router.route('/:review')
 // Handles requests for all germline reviews for a report
 router.route('/')
   .get(async (req, res) => {
-    const key = `/germline/${req.report.ident}/reviews`;
-
-    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 germline reviews ${error}`);
-    }
-
     try {
       const results = await db.models.germlineSmallMutationReview.scope('public').findAll({
         where: {germlineReportId: req.report.id},
       });
 
-      if (key) {
-        cache.set(key, JSON.stringify(results), 'EX', 14400);
-      }
-
       return res.json(results);
     } catch (error) {
       logger.error(`Unable to retrieve germline reviews ${error}`);

diff --git a/app/routes/germlineSmallMutation/variants.js b/app/routes/germlineSmallMutation/variants.js
@@ -5,7 +5,6 @@ const router = express.Router({mergeParams: true});
 
 const db = require('../../models');
 const logger = require('../../log');
-const cache = require('../../cache');
 
 const schemaGenerator = require('../../schemas/schemaGenerator');
 const validateAgainstSchema = require('../../libs/validateAgainstSchema');
@@ -98,28 +97,11 @@ router.route('/:variant')
 // Handles requests for all germline variants for a report
 router.route('/')
   .get(async (req, res) => {
-    const key = `/germline/${req.report.ident}/variants`;
-
-    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 germline variants ${error}`);
-    }
-
     try {
       const results = await db.models.germlineSmallMutationVariant.scope('public').findAll({
         where: {germlineReportId: req.report.id},
       });
 
-      if (key) {
-        cache.set(key, JSON.stringify(results), 'EX', 14400);
-      }
-
       return res.json(results);
     } catch (error) {
       logger.error(`Unable to retrieve germline variants ${error}`);

diff --git a/app/routes/report/gene.js b/app/routes/report/gene.js
@@ -11,9 +11,12 @@ const router = express.Router({mergeParams: true});
 
 const schemaGenerator = require('../../schemas/schemaGenerator');
 const validateAgainstSchema = require('../../libs/validateAgainstSchema');
-const {REPORT_UPDATE_BASE_URI} = require('../../constants');
+const {REPORT_CREATE_BASE_URI, REPORT_UPDATE_BASE_URI} = require('../../constants');
 
 // Generate schemas
+const createSchema = schemaGenerator(db.models.genes, {
+  baseUri: REPORT_CREATE_BASE_URI,
+});
 const updateSchema = schemaGenerator(db.models.genes, {
   baseUri: REPORT_UPDATE_BASE_URI, nothingRequired: true,
 });
@@ -138,6 +141,30 @@ router.route('/')
         error: {message: 'Unable to retrieve genes'},
       });
     }
+  })
+  .post(async (req, res) => {
+    // Validate request against schema
+    try {
+      validateAgainstSchema(createSchema, req.body);
+    } catch (error) {
+      const message = `Error while validating gene create request ${error}`;
+      logger.error(message);
+      return res.status(HTTP_STATUS.BAD_REQUEST).json({error: {message}});
+    }
+
+    // Create new entry in db
+    try {
+      const result = await db.models.genes.create({
+        ...req.body,
+        reportId: req.report.id,
+      });
+      return res.status(HTTP_STATUS.CREATED).json(result.view('public'));
+    } catch (error) {
+      logger.error(`Unable to create gene ${error}`);
+      return res.status(HTTP_STATUS.INTERNAL_SERVER_ERROR).json({
+        error: {message: 'Unable to create gene'},
+      });
+    }
   });
 
 module.exports = router;
diff --git a/app/routes/report/report.js b/app/routes/report/report.js
@@ -105,7 +105,7 @@ router.route('/')
   .get(async (req, res) => {
     let {
       query: {
-        paginated, limit, offset, sort, project, states, role, searchText, keyVariant, matchingThreshold, category, approvedTherapy, kbVariant, disease, relevance, context, status, reference, sample, evidenceLevel, matchedCancer, pmidRef, variantType,
+        paginated, limit, offset, sort, project, states, role, searchText, keyVariant, matchingThreshold, kbVariant,
       },
     } = req;
 
@@ -125,7 +125,7 @@ router.route('/')
     try {
       // validate request query parameters
       validateAgainstSchema(reportGetSchema, {
-        paginated, limit, offset, sort, project, states, role, searchText, keyVariant, matchingThreshold, category, approvedTherapy, kbVariant, disease, relevance, context, status, reference, sample, evidenceLevel, matchedCancer, pmidRef, variantType,
+        paginated, limit, offset, sort, project, states, role, searchText, keyVariant, matchingThreshold, kbVariant,
       }, false);
     } catch (err) {
       const message = `Error while validating the query params of the report GET request ${err}`;
@@ -184,15 +184,12 @@ router.route('/')
         ...((kbVariant && matchingThreshold) ? {
           '$kbMatches.kb_variant$': {
             [Op.in]: literal(
-              `(SELECT "kb_variant" 
-              FROM (SELECT "kb_variant", word_similarity('${kbVariant}', "kb_variant") FROM reports_kb_matches) AS subquery 
+              `(SELECT "kb_variant"
+              FROM (SELECT "kb_variant", word_similarity('${kbVariant}', "kb_variant") FROM reports_kb_matches) AS subquery
               WHERE word_similarity >= ${matchingThreshold})`,
             ),
           },
         } : {}),
-        ...((variantType) ? {
-          '$kbMatches.variant_type$': {[Op.eq]: `${variantType}`},
-        } : {}),
       },
       distinct: 'id',
       // **searchText with paginated with patientInformation set to required: true
@@ -262,51 +259,9 @@ router.route('/')
           model: db.models.genomicAlterationsIdentified.scope('public'),
           as: 'genomicAlterationsIdentified',
         }] : []),
-        ...((category || approvedTherapy || kbVariant || disease || relevance || context || status || reference || sample || evidenceLevel || matchedCancer || pmidRef || variantType) ? [{
-          model: db.models.kbMatches.scope('public'),
+        ...((kbVariant && matchingThreshold) ? [{
+          model: db.models.kbMatches.scope('minimal'),
           as: 'kbMatches',
-          include: [
-            {
-              model: db.models.kbMatchedStatements.scope('kbMatchesInclude'),
-              as: 'kbMatchedStatements',
-              through: {attributes: []},
-              where: {
-                ...((category) ? {
-                  category: {[Op.eq]: `${category}`},
-                } : {}),
-                ...((approvedTherapy) ? {
-                  approvedTherapy: {[Op.eq]: `${approvedTherapy}`},
-                } : {}),
-                ...((disease) ? {
-                  disease: {[Op.eq]: `${disease}`},
-                } : {}),
-                ...((relevance) ? {
-                  relevance: {[Op.eq]: `${relevance}`},
-                } : {}),
-                ...((context) ? {
-                  context: {[Op.eq]: `${context}`},
-                } : {}),
-                ...((status) ? {
-                  status: {[Op.eq]: `${status}`},
-                } : {}),
-                ...((reference) ? {
-                  reference: {[Op.eq]: `${reference}`},
-                } : {}),
-                ...((sample) ? {
-                  sample: {[Op.eq]: `${sample}`},
-                } : {}),
-                ...((evidenceLevel) ? {
-                  evidence_level: {[Op.eq]: `${evidenceLevel}`},
-                } : {}),
-                ...((matchedCancer) ? {
-                  matched_cancer: {[Op.eq]: `${matchedCancer}`},
-                } : {}),
-                ...((pmidRef) ? {
-                  pmid_ref: {[Op.eq]: `${pmidRef}`},
-                } : {}),
-              },
-            },
-          ],
         }] : []),
       ],
     };

diff --git a/app/routes/report/tmburMutationBurden.js b/app/routes/report/tmburMutationBurden.js
@@ -71,7 +71,7 @@ router.route('/')
   .post(async (req, res) => {
     // Validate request against schema
     try {
-      await validateAgainstSchema(createSchema, req.body);
+      validateAgainstSchema(createSchema, req.body);
     } catch (error) {
       const message = `Error while validating tmbur mutation burden create request ${error}`;
       logger.error(message);

diff --git a/test/routes/report/gene.test.js b/test/routes/report/gene.test.js
@@ -97,7 +97,7 @@ describe('/reports/{report}/genes', () => {
     afterEach(async () => {
       return db.models.genes.destroy({
         where: {ident: getGene.ident},
-        force: true,
+        // force: true,
       });
     });
 
@@ -162,6 +162,50 @@ describe('/reports/{report}/genes', () => {
     });
   });
 
+  describe('POST', () => {
+    test('/ - 201 Created', async () => {
+      const res = await request
+        .post(`/api/reports/${report.ident}/genes`)
+        .send(GENE_DATA)
+        .auth(username, password)
+        .type('json')
+        .expect(HTTP_STATUS.CREATED);
+
+      checkGene(res.body);
+      expect(res.body).toEqual(expect.objectContaining(GENE_DATA));
+
+      // Check that record was created in the db
+      const result = await db.models.genes.findOne({
+        where: {ident: res.body.ident},
+      });
+      expect(result).not.toBeNull();
+
+      // Delete entry
+      await result.destroy({force: true});
+    });
+
+    test('/ - 400 Bad Request - Additional Property', async () => {
+      await request
+        .post(`/api/reports/${report.ident}/genes`)
+        .send({
+          ...GENE_UPDATE_DATA,
+          additionalProperty: 'ADDITIONAL_PROPERTY',
+        })
+        .auth(username, password)
+        .type('json')
+        .expect(HTTP_STATUS.BAD_REQUEST);
+    });
+
+    test('/ - 400 Bad Request - Gene name is required', async () => {
+      await request
+        .post(`/api/reports/${report.ident}/genes`)
+        .send({})
+        .auth(username, password)
+        .type('json')
+        .expect(HTTP_STATUS.BAD_REQUEST);
+    });
+  });
+
   describe('PUT', () => {
     let putGene;
 

diff --git a/test/routes/report/report.test.js b/test/routes/report/report.test.js
@@ -68,6 +68,7 @@ describe('/reports/{REPORTID}', () => {
   const UNREVIEWED_ACCESS = 'unreviewed Access';
 
   const KEYVARIANT = 'uniqueKeyVariant';
+  const KBVARIANT = 'uniqueKbVariant';
 
   let project;
   let project2;
@@ -503,7 +504,7 @@ describe('/reports/{REPORTID}', () => {
 
     test('/ - kb match - 200 Success', async () => {
       const res = await request
-        .get('/api/reports?category=unknown&variantType=cnv')
+        .get(`/api/reports?kbVariant=${KBVARIANT}&&matchingThreshold=1`)
         .auth(username, password)
         .type('json')
         .expect(HTTP_STATUS.OK);
@@ -512,7 +513,7 @@ describe('/reports/{REPORTID}', () => {
 
       for (const resReport of res.body.reports) {
         for (const gAI of resReport.kbMatches) {
-          expect(gAI.variantType).toEqual('cnv');
+          expect(gAI.kbVariant).toEqual(KBVARIANT);
         }
       }
     }, LONGER_TIMEOUT);