Merge pull request #360 from hms-dbmi-cellenics/plots-and-tables-v2

[BIOMAGE-1880] - Plots and tables v2

src/api.v2/controllers/__mocks__/plotController.js

@@ -0,0 +1,7 @@
+const mockGetPlotConfig = jest.fn();
+const mockUpdatePlotConfig = jest.fn();
+
+module.exports = {
+  getPlotConfig: mockGetPlotConfig,
+  updatePlotConfig: mockUpdatePlotConfig,
+};

src/api.v2/controllers/plotController.js

@@ -0,0 +1,34 @@
+const getLogger = require('../../utils/getLogger');
+const { OK } = require('../../utils/responses');
+
+const Plot = require('../model/Plot');
+
+const logger = getLogger('[Plot Controller] - ');
+
+const getPlotConfig = async (req, res) => {
+  const { experimentId, plotUuid } = req.params;
+  logger.log(`Getting plot config for plot ${plotUuid}`);
+
+  const result = await new Plot().getConfig(experimentId, plotUuid);
+
+  logger.log(`Finished getting config for plot ${plotUuid}`);
+  res.json(result);
+};
+
+const updatePlotConfig = async (req, res) => {
+  const { experimentId, plotUuid } = req.params;
+  const { config } = req.body;
+
+  logger.log(`Updating config for plot ${plotUuid}`);
+
+  await new Plot().updateConfig(experimentId, plotUuid, config);
+
+  logger.log(`Finished updating config for plot ${plotUuid}`);
+
+  res.send(OK());
+};
+
+module.exports = {
+  getPlotConfig,
+  updatePlotConfig,
+};

src/api.v2/helpers/s3/bucketNames.js

@@ -5,6 +5,7 @@ const bucketNames = {
   PROCESSED_MATRIX: `processed-matrix-${config.clusterEnv}`,
   RAW_SEURAT: `biomage-source-${config.clusterEnv}`,
   CELL_SETS: `cell-sets-${config.clusterEnv}`,
+  PLOTS: `plots-tables-${config.clusterEnv}`,
 };
 
 module.exports = bucketNames;

src/api.v2/model/Plot.js

@@ -1,7 +1,11 @@
 const BasicModel = require('./BasicModel');
 const sqlClient = require('../../sql/sqlClient');
 
+const validateRequest = require('../../utils/schema-validator');
+
 const tableNames = require('./tableNames');
+const bucketNames = require('../helpers/s3/bucketNames');
+const getObject = require('../helpers/s3/getObject');
 
 const selectableProps = [
   'id',
@@ -14,6 +18,37 @@ class Plot extends BasicModel {
   constructor(sql = sqlClient.get()) {
     super(sql, tableNames.PLOT, selectableProps);
   }
+
+  async getConfig(experimentId, plotUuid) {
+    const {
+      s3DataKey,
+      config: plotConfig,
+    } = await this.findOne({ id: plotUuid, experiment_id: experimentId });
+
+    const result = { config: plotConfig };
+
+
+    if (s3DataKey) {
+      const plotDataObject = await getObject({
+        Bucket: bucketNames.PLOTS,
+        Key: s3DataKey,
+      });
+
+      const output = JSON.parse(plotDataObject);
+
+      if (output.plotData) {
+        await validateRequest(output, 'plots-bodies/PlotData.v2.yaml');
+      }
+
+      result.plotData = output.plotData || [];
+    }
+
+    return result;
+  }
+
+  async updateConfig(experimentId, plotUuid, plotConfig) {
+    return await this.update({ id: plotUuid, experiment_id: experimentId }, { config: plotConfig });
+  }
 }
 
 module.exports = Plot;

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

@@ -0,0 +1,11 @@
+const BasicModel = require('./BasicModel')();
+
+const stub = {
+  getConfig: jest.fn(),
+  updateConfig: jest.fn(),
+  ...BasicModel,
+};
+
+const Plot = jest.fn().mockImplementation(() => stub);
+
+module.exports = Plot;

src/api.v2/routes/plots.js

@@ -0,0 +1,17 @@
+const {
+  getPlotConfig,
+  updatePlotConfig,
+} = require('../controllers/plotController');
+
+const { expressAuthorizationMiddleware } = require('../middlewares/authMiddlewares');
+
+module.exports = {
+  'plots#get': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => getPlotConfig(req, res).catch(next),
+  ],
+  'plots#update': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => updatePlotConfig(req, res).catch(next),
+  ],
+};

src/specs/api.v2.yaml

@@ -1153,6 +1153,101 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/HTTPError'
+  '/experiments/{experimentId}/plots/{plotUuid}':
+    parameters:
+      - schema:
+          type: string
+        name: plotUuid
+        in: path
+        required: true
+      - schema:
+          type: string
+        name: experimentId
+        in: path
+        required: true
+    get:
+      summary: Get a plot or table config
+      operationId: getPlotTable
+      x-eov-operation-id: plots#get
+      x-eov-operation-handler: routes/plots
+      responses:
+        '200':
+          description: OK
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/PlotConfig'
+        '400':
+          description: Bad request
+          content:
+            application/json:
+              schema:
+                $ref: ./models/HTTPError.v1.yaml
+        '401':
+          description: The request lacks authentication credentials.
+          content:
+            application/json:
+              schema:
+                $ref: ./models/HTTPError.v1.yaml
+        '403':
+          description: The authenticated user is not authorized to view this resource.
+          content:
+            application/json:
+              schema:
+                $ref: ./models/HTTPError.v1.yaml
+        '404':
+          description: Experiment/plot not found.
+          content:
+            application/json:
+              schema:
+                $ref: ./models/HTTPError.v1.yaml
+      description: Reads a plot and table for a given experiment with the data specified.
+    put:
+      summary: Update a plot or table config
+      operationId: updatePlotTable
+      x-eov-operation-id: plots#update
+      x-eov-operation-handler: routes/plots
+      responses:
+        '200':
+          description: Update to object in response successful.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPSuccess'
+        '201':
+          description: New resource created.
+          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: The authenticated user is not authorized to view this resource.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPError'
+        '404':
+          description: Invalid experiment ID specified.
+      description: Updates a plot and table for a given experiment with the data specified.
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/PlotConfig'
+        description: The new configuration to update the old one by.
+
   '/experiments/{experimentId}/qc':
     parameters:
       - schema:
@@ -1190,7 +1285,8 @@ paths:
           content:
             application/json:
               schema:
-                $ref: ./models/HTTPError.v1.yaml
+                $ref: '#/components/schemas/HTTPError'
+
   /gem2sResults:
     post:
       summary: Retrieve results from pipeline step functions
@@ -1345,6 +1441,8 @@ components:
       $ref: './models/samples-bodies/PatchSampleFile.v2.yaml'
     CellSets:
       $ref: ./models/cell-sets-bodies/CellSets.v2.yaml
+    PlotConfig:
+      $ref: ./models/plots-bodies/PlotConfig.v2.yaml
     HTTPSuccess:
       $ref: './models/HTTPSuccess.v1.yaml'
     HTTPError:

src/specs/models/plots-bodies/PlotConfig.v2.yaml

@@ -0,0 +1,8 @@
+title: Plots and tables configuration
+type: object
+description: A file specifying the configuration for a given plot/table.
+properties:
+  config:
+    type: object
+required:
+  - config

src/specs/models/plots-bodies/PlotData.v2.yaml

@@ -0,0 +1,10 @@
+title: Plot Data
+type: object
+properties:
+  plotData:
+    anyOf:
+      - type: array
+      - type: object
+required:
+  - plotData
+description: Object storing the data for one particular plot.

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

@@ -0,0 +1,69 @@
+// Disable semantic check because linter doesn't recognize jest mocks
+// @ts-nocheck
+const plotController = require('../../../src/api.v2/controllers/plotController');
+const Plot = require('../../../src/api.v2/model/Plot');
+
+const { OK } = require('../../../src/utils/responses');
+
+jest.mock('../../../src/api.v2/model/Plot');
+
+const mockRes = {
+  json: jest.fn(),
+  send: jest.fn(),
+};
+
+const mockExperimentId = 'experimentId';
+const mockPlotUuid = 'plotUuid';
+
+const plotInstance = new Plot();
+
+describe('plotController', () => {
+  beforeEach(async () => {
+    jest.clearAllMocks();
+  });
+
+  it('getting plot works correctly', async () => {
+    const mockConfig = {
+      experimentId: mockExperimentId,
+      plotUuid: mockPlotUuid,
+      plotType: 'SomePlotType',
+      config: {},
+    };
+
+    plotInstance.getConfig.mockReturnValue(mockConfig);
+
+    const mockReq = {
+      params: { experimentId: mockExperimentId, plotUuid: mockPlotUuid },
+    };
+
+    await plotController.getPlotConfig(mockReq, mockRes);
+
+    expect(plotInstance.getConfig).toHaveBeenCalledWith(
+      mockExperimentId, mockPlotUuid,
+    );
+
+    expect(mockRes.json).toHaveBeenCalledWith(mockConfig);
+  });
+
+  it('updating plot works correctly', async () => {
+    const mockConfig = {
+      experimentId: mockExperimentId,
+      plotUuid: mockPlotUuid,
+      plotType: 'SomePlotType',
+      config: {},
+    };
+
+    const mockReq = {
+      params: { experimentId: mockExperimentId, plotUuid: mockPlotUuid },
+      body: { config: mockConfig },
+    };
+
+    await plotController.updatePlotConfig(mockReq, mockRes);
+
+    expect(plotInstance.updateConfig).toHaveBeenCalledWith(
+      mockExperimentId, mockPlotUuid, mockConfig,
+    );
+
+    expect(mockRes.send).toHaveBeenCalledWith(OK());
+  });
+});

tests/api.v2/helpers/access/createUserInvite.test.js

@@ -42,8 +42,6 @@ describe('creatUserInvite', () => {
 
     expect(sendEmail).toHaveBeenCalledTimes(1);
 
-    console.log('*** calls', sendEmail.mock.calls);
-
     const emailBody = sendEmail.mock.calls[0][0];
 
     expect(emailBody).toMatchSnapshot();