Merge pull request #334 from hms-dbmi-cellenics/1835-samples-patch-ap…

…i-v2

[BIOMAGE-1835] Implement samples PATCH for api v2

src/api.v2/controllers/experimentController.js

@@ -53,13 +53,13 @@ const createExperiment = async (req, res) => {
 const patchExperiment = async (req, res) => {
   const { params: { experimentId }, body } = req;
 
-  logger.log(`Updating experiment ${experimentId}`);
+  logger.log(`Patching experiment ${experimentId}`);
 
   const snakeCasedKeysToPatch = _.mapKeys(body, (_value, key) => _.snakeCase(key));
 
   await new Experiment().updateById(experimentId, snakeCasedKeysToPatch);
 
-  logger.log(`Finished updating experiment ${experimentId}`);
+  logger.log(`Finished patching experiment ${experimentId}`);
 
   res.json(OK());
 };

src/api.v2/controllers/sampleController.js

@@ -1,3 +1,5 @@
+const _ = require('lodash');
+
 const Sample = require('../model/Sample');
 const Experiment = require('../model/Experiment');
 const MetadataTrack = require('../model/MetadataTrack');
@@ -36,9 +38,25 @@ const createSample = async (req, res) => {
   res.json(OK());
 };
 
+const patchSample = async (req, res) => {
+  const { params: { experimentId, sampleId }, body } = req;
+
+  logger.log(`Patching sample ${sampleId} in experiment ${experimentId}`);
+
+  const snakeCasedKeysToPatch = _.mapKeys(body, (_value, key) => _.snakeCase(key));
+
+  await new Sample().updateById(sampleId, snakeCasedKeysToPatch);
+
+  logger.log(`Finished patching sample ${sampleId} in experiment ${experimentId}`);
+
+  res.json(OK());
+};
+
 const deleteSample = async (req, res) => {
   const { params: { experimentId, sampleId } } = req;
 
+  logger.log(`Deleting sample ${sampleId} from experiment ${experimentId}`);
+
   await sqlClient.get().transaction(async (trx) => {
     await new Sample(trx).destroy(sampleId);
     await new Experiment(trx).deleteSample(experimentId, sampleId);
@@ -51,5 +69,6 @@ const deleteSample = async (req, res) => {
 
 module.exports = {
   createSample,
+  patchSample,
   deleteSample,
 };

src/api.v2/routes/sample.js

@@ -1,5 +1,6 @@
 const {
   createSample,
+  patchSample,
   deleteSample,
 } = require('../controllers/sampleController');
 
@@ -10,6 +11,10 @@ module.exports = {
     expressAuthorizationMiddleware,
     (req, res, next) => createSample(req, res).catch(next),
   ],
+  'sample#patchSample': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => patchSample(req, res).catch(next),
+  ],
   'sample#deleteSample': [
     expressAuthorizationMiddleware,
     (req, res, next) => deleteSample(req, res).catch(next),

src/specs/api.v2.yaml

@@ -168,7 +168,7 @@ paths:
         content:
           application/json:
             schema:
-              $ref: '#/components/schemas/ExperimentPatch'
+              $ref: '#/components/schemas/PatchExperiment'
       responses:
         '200':
           description: Create experiment
@@ -283,6 +283,52 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/HTTPError'
+    patch:
+      summary: Patch sample
+      operationId: patchSample
+      x-eov-operation-id: sample#patchSample
+      x-eov-operation-handler: routes/sample
+      requestBody:
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                name:
+                  type: string
+              additionalProperties: false
+      responses:
+        '200':
+          description: Success
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPSuccess'
+        '400':
+          description: Bad Request
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '401':
+          description: The request lacks authentication credentials.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '403':
+          description: Forbidden request for this user.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '404':
+          description: Not found error.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+
     delete:
       summary: Delete sample
       operationId: deleteSample
@@ -377,8 +423,8 @@ components:
       $ref: './models/experiment-bodies/CreateExperiment.v2.yaml'
     ExperimentInfo:
       $ref: './models/experiment-bodies/ExperimentInfo.v2.yaml'
-    ExperimentPatch:
-      $ref: './models/experiment-bodies/ExperimentPatch.v2.yaml'
+    PatchExperiment:
+      $ref: './models/experiment-bodies/PatchExperiment.v2.yaml'
     GetAllExperiments:
       $ref: './models/experiment-bodies/GetAllExperiments.v2.yaml'
     CreateSample:

src/specs/models/experiment-bodies/ExperimentPatch.v2.yaml → src/specs/models/experiment-bodies/PatchExperiment.v2.yaml

@@ -1,4 +1,4 @@
-title: Experiment Patch
+title: Patch Experiment 
 description: The properties of an experiment that can be patched
 type: object
 properties:

tests/api.v2/controllers/sampleController.test.js

@@ -123,4 +123,22 @@ describe('sampleController', () => {
 
     expect(mockRes.json).not.toHaveBeenCalled();
   });
+
+  it('patchSample works correctly', async () => {
+    const mockSampleNewName = 'theNewName';
+    const mockReq = {
+      params: { experimentId: mockExperimentId, sampleId: mockSampleId },
+      body: { name: mockSampleNewName },
+    };
+
+    sampleInstance.updateById.mockImplementationOnce(() => Promise.resolve());
+
+    await sampleController.patchSample(mockReq, mockRes);
+
+    expect(sampleInstance.updateById).toHaveBeenCalledWith(
+      mockSampleId, { name: mockSampleNewName },
+    );
+
+    expect(mockRes.json).toHaveBeenCalledWith(OK());
+  });
 });

tests/api.v2/routes/sample.test.js

@@ -10,6 +10,7 @@ const sampleController = require('../../../src/api.v2/controllers/sampleControll
 jest.mock('../../../src/api.v2/controllers/sampleController', () => ({
   createSample: jest.fn(),
   deleteSample: jest.fn(),
+  patchSample: jest.fn(),
 }));
 
 jest.mock('../../../src/api.v2/middlewares/authMiddlewares');
@@ -89,13 +90,8 @@ describe('tests for experiment route', () => {
       return Promise.resolve();
     });
 
-    const invalidExperimentData = {
-      description: 'experimentDescription',
-    };
-
     request(app)
       .delete(`/v2/experiments/${experimentId}/samples/${sampleId}`)
-      .send(invalidExperimentData)
       .expect(200)
       .end((err) => {
         if (err) {
@@ -106,4 +102,44 @@ describe('tests for experiment route', () => {
         return done();
       });
   });
+
+  it('Patching a sample works', async (done) => {
+    sampleController.patchSample.mockImplementationOnce((req, res) => {
+      res.json(OK());
+      return Promise.resolve();
+    });
+
+    request(app)
+      .patch(`/v2/experiments/${experimentId}/samples/${sampleId}`)
+      .send({ name: 'newSampleName' })
+      .expect(200)
+      .end((err) => {
+        if (err) {
+          return done(err);
+        }
+        // there is no point testing for the values of the response body
+        // - if something is wrong, the schema validator will catch it
+        return done();
+      });
+  });
+
+  it('Patching a sample fails if requestBody is invalid', async (done) => {
+    sampleController.patchSample.mockImplementationOnce((req, res) => {
+      res.json(OK());
+      return Promise.resolve();
+    });
+
+    request(app)
+      .patch(`/v2/experiments/${experimentId}/samples/${sampleId}`)
+      .send({ aName: 'newSampleName' })
+      .expect(400)
+      .end((err) => {
+        if (err) {
+          return done(err);
+        }
+        // there is no point testing for the values of the response body
+        // - if something is wrong, the schema validator will catch it
+        return done();
+      });
+  });
 });