Merge pull request #486 from bcgsc/feature/DEVSU-2804-add-variant-fks-genomic-alterations

Feature/devsu 2804 add variant fks genomic alterations

Author: elewis2

app/models/reports/genomic/summary/genomicAlterationsIdentified.js

@@ -37,7 +37,7 @@ module.exports = (sequelize, Sq) => {
     scopes: {
       public: {
         attributes: {
-          exclude: ['id', 'reportId', 'deletedAt', 'updatedBy'],
+          exclude: ['id', 'reportId', 'variantId', 'deletedAt', 'updatedBy'],
         },
       },
     },

app/routes/report/summary/genomicAlterationsIdentified.js

@@ -15,10 +15,10 @@ const {REPORT_CREATE_BASE_URI, REPORT_UPDATE_BASE_URI} = require('../../../const
 
 // Generate schemas
 const createSchema = schemaGenerator(db.models.genomicAlterationsIdentified, {
-  baseUri: REPORT_CREATE_BASE_URI,
+  baseUri: REPORT_CREATE_BASE_URI, additionalProperties: true,
 });
 const updateSchema = schemaGenerator(db.models.genomicAlterationsIdentified, {
-  baseUri: REPORT_UPDATE_BASE_URI, nothingRequired: true,
+  baseUri: REPORT_UPDATE_BASE_URI, nothingRequired: true, additionalProperties: true,
 });
 
 // Middleware for genomic alterations
@@ -40,7 +40,15 @@ router.route('/:alteration([A-z0-9-]{36})')
     }
 
     try {
-      await req.alteration.update(req.body, {userId: req.user.id});
+      let variantId;
+      if (req.body.variantIdent) {
+        const modelName = KB_PIVOT_MAPPING[req.body.variantType];
+        const variant = await db.models[modelName].findOne({
+          where: {ident: req.body.variantIdent},
+        });
+        variantId = variant.id;
+      }
+      await req.alteration.update({...req.body, variantId}, {userId: req.user.id});
       return res.json(req.alteration.view('public'));
     } catch (error) {
       logger.error(`Unable to update genomic alterations ${error}`);
@@ -115,8 +123,15 @@ router.route('/')
 
     try {
       req.body.reportId = req.report.id;
-
-      const result = await db.models.genomicAlterationsIdentified.create(req.body);
+      let variantId;
+      if (req.body.variantIdent) {
+        const modelName = KB_PIVOT_MAPPING[req.body.variantType];
+        const variant = await db.models[modelName].findOne({
+          where: {ident: req.body.variantIdent},
+        });
+        variantId = variant.id;
+      }
+      const result = await db.models.genomicAlterationsIdentified.create({...req.body, variantId});
       return res.status(HTTP_STATUS.CREATED).json(result.view('public'));
     } catch (error) {
       logger.error(`Unable to create genomic alteration entry ${error}`);

package-lock.json

@@ -1,27 +1,17 @@
 const getPort = require('get-port');
 const supertest = require('supertest');
 const HTTP_STATUS = require('http-status-codes');
-
 const db = require('../../../../app/models');
+const {KB_PIVOT_MAPPING} = require('../../../../app/constants');
 // get test user info
 const CONFIG = require('../../../../app/config');
 const {listen} = require('../../../../app');
 
 CONFIG.set('env', 'test');
 const {username, password} = CONFIG.get('testing');
 
-const ALTERATION_DATA = {
-  geneVariant: 'TEST GENE VARIANT',
-  germline: true,
-};
-
-const ALTERATION_UPDATE_DATA = {
-  geneVariant: 'UPDATED GENE VARIANT',
-  germline: false,
-};
-
 const alterationProperties = [
-  'ident', 'createdAt', 'geneVariant', 'germline',
+  'ident', 'createdAt', 'geneVariant', 'germline', 'variantType',
 ];
 
 const checkAlteration = (alterationObject) => {
@@ -42,8 +32,23 @@ const checkAlterations = (alterations) => {
   });
 };
 
+const CHECKING_DATA = {
+  geneVariant: 'TEST GENE VARIANT',
+  variantType: 'cnv',
+  germline: true,
+};
+
+const CHECKING_UPDATE_DATA = {
+  geneVariant: 'UPDATED GENE VARIANT',
+  variantType: 'cnv',
+  germline: false,
+};
+
 let server;
 let request;
+let variant;
+let ALTERATION_DATA;
+let ALTERATION_UPDATE_DATA;
 
 // Start API
 beforeAll(async () => {
@@ -63,6 +68,23 @@ describe('/reports/{report}/summary/genomic-alterations-identified', () => {
       templateId: template.id,
       patientId: 'PROBE_TEST_PATIENT',
     });
+
+    // Find a random variant for testing
+    const modelName = KB_PIVOT_MAPPING.cnv;
+    variant = await db.models[modelName].findOne();
+    ALTERATION_DATA = {
+      geneVariant: 'TEST GENE VARIANT',
+      variantType: 'cnv',
+      variantIdent: variant.ident,
+      germline: true,
+    };
+
+    ALTERATION_UPDATE_DATA = {
+      geneVariant: 'UPDATED GENE VARIANT',
+      variantType: 'cnv',
+      variantIdent: variant.ident,
+      germline: false,
+    };
   });
 
   afterAll(async () => {
@@ -130,7 +152,7 @@ describe('/reports/{report}/summary/genomic-alterations-identified', () => {
         .expect(HTTP_STATUS.CREATED);
 
       checkAlteration(res.body);
-      expect(res.body).toEqual(expect.objectContaining(ALTERATION_DATA));
+      expect(res.body).toEqual(expect.objectContaining(CHECKING_DATA));
 
       // Check that record was created in the db
       const result = await db.models.genomicAlterationsIdentified.findOne({
@@ -142,18 +164,6 @@ describe('/reports/{report}/summary/genomic-alterations-identified', () => {
       await result.destroy({force: true});
     });
 
-    test('/ - 400 Bad Request - Additional Property', async () => {
-      await request
-        .post(`/api/reports/${report.ident}/summary/genomic-alterations-identified`)
-        .send({
-          ...ALTERATION_UPDATE_DATA,
-          additionalProperty: 'ADDITIONAL_PROPERTY',
-        })
-        .auth(username, password)
-        .type('json')
-        .expect(HTTP_STATUS.BAD_REQUEST);
-    });
-
     test('/ - 400 Bad Request - Incorrect field type', async () => {
       await request
         .post(`/api/reports/${report.ident}/summary/genomic-alterations-identified`)
@@ -201,19 +211,7 @@ describe('/reports/{report}/summary/genomic-alterations-identified', () => {
 
       expect(res.body).not.toBeNull();
       checkAlteration(res.body);
-      expect(res.body).toEqual(expect.objectContaining(ALTERATION_UPDATE_DATA));
-    });
-
-    test('/{alteration} - 400 Bad Request - Additional Property', async () => {
-      await request
-        .put(`/api/reports/${report.ident}/summary/genomic-alterations-identified/${putAlteration.ident}`)
-        .send({
-          ...ALTERATION_UPDATE_DATA,
-          additionalProperty: 'ADDITIONAL_PROPERTY',
-        })
-        .auth(username, password)
-        .type('json')
-        .expect(HTTP_STATUS.BAD_REQUEST);
+      expect(res.body).toEqual(expect.objectContaining(CHECKING_UPDATE_DATA));
     });
 
     test('/{alteration} - 400 Bad Request - Incorrect field type', async () => {