Merge branch 'develop' into bugfix/DEVSU-2524-reorder-graphkb-evidenc…

…e-levels

app/models/reports/report.js

@@ -26,9 +26,9 @@ module.exports = (sequelize, Sq) => {
       field: 'hrdetect_score',
       type: Sq.FLOAT,
     },
-    intersectTmbScore: {
-      name: 'intersectTmbScore',
-      field: 'intersect_tmb_score',
+    genomeTmb: {
+      name: 'genomeTmb',
+      field: 'genome_tmb',
       type: Sq.FLOAT,
     },
     alternateIdentifier: {

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;

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);

migrations/20241129212739-DEVSU-2513-rename-tbm-score.js

@@ -0,0 +1,15 @@
+const TABLE = 'reports';
+
+module.exports = {
+  up: (queryInterface) => {
+    return queryInterface.sequelize.transaction(async (transaction) => {
+      return Promise.all([
+        queryInterface.renameColumn(TABLE, 'intersect_tmb_score', 'genome_tmb', {transaction}),
+      ]);
+    });
+  },
+
+  down: () => {
+    throw new Error('Not Implemented!');
+  },
+};

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;
 

test/routes/report/report.test.js

@@ -29,7 +29,7 @@ const checkReport = (report) => {
     'biopsyDate', 'biopsyName', 'presentationDate', 'kbDiseaseMatch',
     'kbUrl', 'pediatricIds', 'captiv8Score', 'appendix', 'hrdetectScore',
     'legacyReportFilepath', 'legacyPresentationFilepath', 'signatures',
-    'intersectTmbScore',
+    'genomeTmb',
   ].forEach((element) => {
     expect(report).toHaveProperty(element);
   });

test/routes/report/reportAsync.test.js

@@ -27,7 +27,7 @@ const checkReport = (report) => {
     'state', 'expression_matrix', 'alternateIdentifier', 'ageOfConsent',
     'biopsyDate', 'biopsyName', 'presentationDate', 'kbDiseaseMatch',
     'kbUrl', 'pediatricIds', 'captiv8Score', 'hrdetectScore', 'appendix',
-    'intersectTmbScore',
+    'genomeTmb',
   ].forEach((element) => {
     expect(report).toHaveProperty(element);
   });

test/testData/mockReportData.json

@@ -2,7 +2,7 @@
     "template": "genomic",
     "captiv8Score": 20,
     "hrdetectScore": 10.5,
-    "intersectTmbScore": 9.75,
+    "genomeTmb": 9.75,
     "appendix": "this is an example of an appendix",
     "sampleInfo": [
         {