[BIOMAGE-1804] Implement load & save processing settings for api v2

src/api.v2/controllers/experimentController.js

@@ -82,10 +82,28 @@ 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());
+};
+
 module.exports = {
   getAllExperiments,
   getExperiment,
   createExperiment,
+  updateProcessingConfig,
   patchExperiment,
   updateSamplePosition,
+  getProcessingConfig,
 };

src/api.v2/model/Experiment.js

@@ -144,6 +144,24 @@ class Experiment extends BasicModel {
     }
   }
 
+  async getProcessingConfig(experimentId) {
+    const result = await this.find({ id: experimentId });
+    if (_.isEmpty(result)) {
+      throw new NotFoundError('Experiment not found');
+    }
+
+    return result[0].processingConfig;
+  }
+
+  async updateProcessingConfig(experimentId, body) {
+    const { name: stepName, body: change } = body[0];
+
+    const processingConfig = await this.getProcessingConfig(experimentId);
+    processingConfig[stepName] = change;
+
+    await this.update(experimentId, { processing_config: processingConfig });
+  }
+
   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

@@ -1,5 +1,6 @@
 const {
-  createExperiment, getExperiment, patchExperiment, updateSamplePosition, getAllExperiments,
+  createExperiment, getExperiment, patchExperiment, updateSamplePosition,
+  getAllExperiments, getProcessingConfig, updateProcessingConfig,
 } = require('../controllers/experimentController');
 
 const { expressAuthenticationOnlyMiddleware, expressAuthorizationMiddleware } = require('../middlewares/authMiddlewares');
@@ -25,4 +26,12 @@ 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),
+  ],
 };

src/specs/api.v2.yaml

@@ -58,6 +58,69 @@ 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'
+        '404':
+          description: Not found error.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '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'
+    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'
+        '404':
+          description: Not found error.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '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'
   '/experiments':
     get:
       summary: Get all experiments
@@ -330,6 +393,7 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/HTTPError'
+
 components:
   schemas:
     CreateExperiment:
@@ -338,6 +402,8 @@ components:
       $ref: './models/experiment-bodies/ExperimentInfo.v2.yaml'
     ExperimentPatch:
       $ref: './models/experiment-bodies/ExperimentPatch.v2.yaml'
+    ProcessingConfig:
+      $ref: './models/experiment-bodies/ProcessingConfig.v2.yaml'
     GetAllExperiments:
       $ref: './models/experiment-bodies/GetAllExperiments.v2.yaml'
     CreateSample:

src/specs/models/api-body-schemas/ProcessingConfig.v1.yaml

@@ -2,28 +2,28 @@ title: Processing Config schema
 description: Processing Config schema
 type: object
 properties:
-  cellSizeDistribution:
-    $ref: '../processing-config-bodies/ProcessingConfigCellSizeDistribution.v1.yaml'
-  mitochondrialContent:
-    $ref: '../processing-config-bodies/ProcessingConfigMitochondrialContent.v1.yaml'
-  readAlignment:
-    $ref: '../processing-config-bodies/ProcessingConfigReadAlignment.v1.yaml'
-  classifier:
-    $ref: '../processing-config-bodies/ProcessingConfigClassifier.v1.yaml'
-  numGenesVsNumUmis:
-    $ref: '../processing-config-bodies/ProcessingConfigNumGenesVsNumUMIs.v1.yaml'
-  doubletScores:
-    $ref: '../processing-config-bodies/ProcessingConfigDoubletScores.v1.yaml'
-  dataIntegration:
-    $ref: '../processing-config-bodies/ProcessingConfigDataIntegration.v1.yaml'
-  configureEmbedding:
-    $ref: '../processing-config-bodies/ProcessingConfigConfigureEmbedding.v1.yaml'
+  processingConfig:
+    type: object
+    properties:
+      cellSizeDistribution:
+        $ref: '../processing-config-bodies/ProcessingConfigCellSizeDistribution.v1.yaml'
+      mitochondrialContent:
+        $ref: '../processing-config-bodies/ProcessingConfigMitochondrialContent.v1.yaml'
+      readAlignment:
+        $ref: '../processing-config-bodies/ProcessingConfigReadAlignment.v1.yaml'
+      classifier:
+        $ref: '../processing-config-bodies/ProcessingConfigClassifier.v1.yaml'
+      numGenesVsNumUmis:
+        $ref: '../processing-config-bodies/ProcessingConfigNumGenesVsNumUMIs.v1.yaml'
+      doubletScores:
+        $ref: '../processing-config-bodies/ProcessingConfigDoubletScores.v1.yaml'
+      dataIntegration:
+        $ref: '../processing-config-bodies/ProcessingConfigDataIntegration.v1.yaml'
+      configureEmbedding:
+        $ref: '../processing-config-bodies/ProcessingConfigConfigureEmbedding.v1.yaml'
+
 required:
-  - cellSizeDistribution
-  - mitochondrialContent
-  - readAlignment
-  - classifier
-  - numGenesVsNumUmis
-  - doubletScores
-  - dataIntegration
-  - configureEmbedding
+  - processingConfig: [
+    'cellSizeDistribution', 'mitochondrialContent', 'readAlignment', 
+    'classifier', 'numGenesVsNumUmis', 'doubletScores', 'dataIntegration', 'configureEmbedding']
+additionalProperties: false

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

@@ -172,4 +172,36 @@ 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,
+    );
+  });
 });