Merge branch 'master' into heartbeat

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());
 };
@@ -86,6 +86,22 @@ const updateSamplePosition = async (req, res) => {
   res.json(OK());
 };
 
+const getProcessingConfig = async (req, res) => {
+  const { params: { experimentId } } = req;
+  logger.log('Getting processing config for experiment ', experimentId);
+
+  const result = await new Experiment().getProcessingConfig(experimentId);
+  res.json(result);
+};
+
+const updateProcessingConfig = async (req, res) => {
+  const { params: { experimentId }, body } = req;
+  logger.log('Updating processing config for experiment ', experimentId);
+
+  await new Experiment().updateProcessingConfig(experimentId, body);
+  res.json(OK());
+};
+
 const getBackendStatus = async (req, res) => {
   const { experimentId } = req.params;
 
@@ -114,7 +130,9 @@ module.exports = {
   getAllExperiments,
   getExperiment,
   createExperiment,
+  updateProcessingConfig,
   patchExperiment,
   updateSamplePosition,
+  getProcessingConfig,
   getBackendStatus,
 };

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/model/Experiment.js

@@ -143,6 +143,25 @@ class Experiment extends BasicModel {
     }
   }
 
+  async getProcessingConfig(experimentId) {
+    const result = await this.findOne({ id: experimentId });
+    if (_.isEmpty(result)) {
+      throw new NotFoundError('Experiment not found');
+    }
+
+    return result.processingConfig;
+  }
+
+  async updateProcessingConfig(experimentId, body) {
+    const { name: stepName, body: change } = body[0];
+    const updateString = JSON.stringify({ [stepName]: change });
+
+    await this.sql(tableNames.EXPERIMENT)
+      .update({
+        processing_config: this.sql.raw(`processing_config || '${updateString}'::jsonb`),
+      }).where('id', experimentId);
+  }
+
   async addSample(experimentId, sampleId) {
     await this.sql(tableNames.EXPERIMENT)
       .update({

src/api.v2/model/__mocks__/Experiment.js

@@ -4,6 +4,8 @@ const stub = {
   getAllExperiments: jest.fn(),
   getExperimentData: jest.fn(),
   updateSamplePosition: jest.fn(),
+  updateProcessingConfig: jest.fn(),
+  getProcessingConfig: jest.fn(),
   addSample: jest.fn(),
   deleteSample: jest.fn(),
   ...BasicModel,

src/api.v2/routes/experiment.js

@@ -1,6 +1,6 @@
 const {
-  createExperiment, getExperiment, patchExperiment, getAllExperiments,
-  updateSamplePosition, getBackendStatus,
+  createExperiment, getExperiment, patchExperiment, updateSamplePosition,
+  getAllExperiments, getProcessingConfig, updateProcessingConfig, getBackendStatus,
 } = require('../controllers/experimentController');
 
 const { expressAuthenticationOnlyMiddleware, expressAuthorizationMiddleware } = require('../middlewares/authMiddlewares');
@@ -26,6 +26,14 @@ module.exports = {
     expressAuthorizationMiddleware,
     (req, res, next) => updateSamplePosition(req, res).catch(next),
   ],
+  'experiment#getProcessingConfig': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => getProcessingConfig(req, res).catch(next),
+  ],
+  'experiment#updateProcessingConfig': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => updateProcessingConfig(req, res).catch(next),
+  ],
   'experiment#getBackendStatus': [
     expressAuthorizationMiddleware,
     (req, res, next) => getBackendStatus(req, res).catch(next),

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

@@ -58,6 +58,71 @@ paths:
                   - env
                   - clusterEnv
       description: Returns a status on the health of the API.
+  '/experiments/{experimentId}/processingConfig':
+    get:
+      summary: Get processing configuration for an experiment
+      description: Get processing configuration for an experiment
+      operationId: getProcessingConfig
+      x-eov-operation-id: experiment#getProcessingConfig
+      x-eov-operation-handler: routes/experiment
+      responses:
+        '200':
+          description: get processing configuration for an experiment
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ProcessingConfig'
+        '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'        
+        '404':
+          description: Not found error.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+
+    put:
+      summary: Update processing configuration for an experiment
+      description: Update processing configuration for an experiment
+      operationId: updateProcessingConfig
+      x-eov-operation-id: experiment#updateProcessingConfig
+      x-eov-operation-handler: routes/experiment
+      responses:
+        '200':
+          description: Processing configuration for an experiment
+          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'
+        '404':
+          description: Not found error.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+
   '/experiments':
     get:
       summary: Get all experiments
@@ -168,7 +233,7 @@ paths:
         content:
           application/json:
             schema:
-              $ref: '#/components/schemas/ExperimentPatch'
+              $ref: '#/components/schemas/PatchExperiment'
       responses:
         '200':
           description: Create experiment
@@ -283,6 +348,52 @@ 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
@@ -371,14 +482,17 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/HTTPError'
+
 components:
   schemas:
     CreateExperiment:
       $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'
+    ProcessingConfig:
+      $ref: './models/experiment-bodies/ProcessingConfig.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:

src/specs/models/experiment-bodies/ProcessingConfig.v2.yaml

@@ -25,4 +25,4 @@ required:
   - numGenesVsNumUmis
   - doubletScores
   - dataIntegration
-  - configureEmbedding
+  - configureEmbedding

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

@@ -177,6 +177,38 @@ describe('experimentController', () => {
     expect(experimentInstance.updateSamplePosition).not.toHaveBeenCalled();
   });
 
+  it('getProcessingConfig works', async () => {
+    const mockReq = {
+      params: {
+        experimentId: mockExperiment.id,
+      },
+    };
+    experimentInstance.getProcessingConfig.mockImplementationOnce(() => Promise.resolve());
+
+    await experimentController.getProcessingConfig(mockReq, mockRes);
+    expect(experimentInstance.getProcessingConfig).toHaveBeenCalledWith(mockExperiment.id);
+  });
+
+  it('updateProcessingConfig works', async () => {
+    const mockReq = {
+      params: {
+        experimentId: mockExperiment.id,
+      },
+      body: [{
+        name: 'classifier',
+        body: {
+          someChangedField: 'a value',
+        },
+      }],
+    };
+    experimentInstance.updateProcessingConfig.mockImplementationOnce(() => Promise.resolve());
+
+    await experimentController.updateProcessingConfig(mockReq, mockRes);
+    expect(experimentInstance.updateProcessingConfig).toHaveBeenCalledWith(
+      mockExperiment.id, mockReq.body,
+    );
+  });
+
   it('getBackendStatus works correctly', async () => {
     getPipelineStatus
       .mockImplementationOnce(() => Promise.resolve('gem2sStatus'))

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());
+  });
 });