Flag disable classifier filter

src/api/route-services/__mocks__/samples.js

@@ -0,0 +1,25 @@
+const mockGetSamples = jest.fn(() => new Promise((resolve) => {
+  resolve({
+    samples: {
+      ids: ['sample-1'],
+      'sample-1': {
+        name: 'sample-1',
+      },
+    },
+  });
+}));
+
+const mockGetSampleIds = jest.fn(() => new Promise((resolve) => {
+  resolve({
+    samples: {
+      ids: ['sample-1', 'sample-2'],
+    },
+  });
+}));
+
+const mock = jest.fn().mockImplementation(() => ({
+  getSamples: mockGetSamples,
+  getSampleIds: mockGetSampleIds,
+}));
+
+module.exports = mock;

src/api/routes/samples.js

@@ -0,0 +1,11 @@
+const SamplesService = require('../route-services/samples');
+
+const samplesService = new SamplesService();
+
+module.exports = {
+  'samples#get': (req, res, next) => {
+    samplesService.getSamples(req.params.experimentId)
+      .then((data) => res.json(data))
+      .catch(next);
+  },
+};

src/specs/api.yaml

@@ -5,7 +5,7 @@ info:
   description: The main Node.js pipeline API.
   license:
     name: MIT
-    url: 'https://github.com/biomage-ltd/api/blob/master/LICENSE'
+    url: "https://github.com/biomage-ltd/api/blob/master/LICENSE"
   contact:
     name: Biomage Ltd.
 servers:
@@ -26,10 +26,10 @@ paths:
         - heartbeat
       summary: API health check
       operationId: checkHealth
-      x-eov-operation-id: 'health#check'
+      x-eov-operation-id: health#check
       x-eov-operation-handler: routes/health
       responses:
-        '200':
+        "200":
           description: API is available.
           content:
             application/json:
@@ -61,10 +61,10 @@ paths:
   /workResults:
     post:
       operationId: receiveWork
-      x-eov-operation-id: 'work#response'
+      x-eov-operation-id: work#response
       x-eov-operation-handler: routes/work
       requestBody:
-        description: The results from the execution of a work request, sent via SNS.
+        description: "The results from the execution of a work request, sent via SNS."
         required: true
         content:
           text/plain:
@@ -77,14 +77,14 @@ paths:
               properties: {}
             examples: {}
       responses:
-        '200':
-          description: 'A JSON-parseable was received by the server, *irrespective of whether it was correct/acceptable or not*.'
+        "200":
+          description: "A JSON-parseable was received by the server, *irrespective of whether it was correct/acceptable or not*."
           content:
             text/plain:
               schema:
                 type: string
                 pattern: ok
-        '500':
+        "500":
           description: The data sent by the server could not be parsed as JSON.
           content:
             text/plain:
@@ -104,10 +104,10 @@ paths:
   /pipelineResults:
     post:
       operationId: receivePipelineResponse
-      x-eov-operation-id: 'pipelines#response'
+      x-eov-operation-id: pipelines#response
       x-eov-operation-handler: routes/pipelines
       requestBody:
-        description: The results from the execution of a pipeline step, sent via SNS.
+        description: "The results from the execution of a pipeline step, sent via SNS."
         required: true
         content:
           text/plain:
@@ -120,14 +120,14 @@ paths:
               properties: {}
             examples: {}
       responses:
-        '200':
-          description: 'A JSON-parseable was received by the server, *irrespective of whether it was correct/acceptable or not*.'
+        "200":
+          description: "A JSON-parseable was received by the server, *irrespective of whether it was correct/acceptable or not*."
           content:
             text/plain:
               schema:
                 type: string
                 pattern: ok
-        '500':
+        "500":
           description: The data sent by the server could not be parsed as JSON.
           content:
             text/plain:
@@ -144,23 +144,23 @@ paths:
       tags:
         - work
     parameters: []
-  '/experiments/{experimentId}':
+  "/experiments/{experimentId}":
     get:
       tags:
         - experiments
       summary: Get experiment details
       description: Returns the main details of the experiment.
       operationId: getExperimentById
-      x-eov-operation-id: 'experiment#findByID'
+      x-eov-operation-id: experiment#findByID
       x-eov-operation-handler: routes/experiment
       responses:
-        '200':
-          description: successful operation
+        "200":
+          description: "Fetch successful, response below"
           content:
             application/json:
               schema:
                 $ref: ./models/api-body-schemas/Experiment.v1.yaml
-        '404':
+        "404":
           description: Experiment not found
           content:
             application/json:
@@ -173,18 +173,18 @@ paths:
         in: path
         required: true
         description: ID of the experiment to find.
-  '/experiments/{experimentId}/cellSets':
+  "/experiments/{experimentId}/cellSets":
     get:
       tags:
         - experiments
       summary: Get cell sets for experiment
       description: Returns a hirearchical view of cell sets in the experiment.
       operationId: getExperimentCellSetsById
-      x-eov-operation-id: 'experiment#getCellSets'
+      x-eov-operation-id: experiment#getCellSets
       x-eov-operation-handler: routes/experiment
       responses:
-        '200':
-          description: 'Request successful, hierarchy returned below.'
+        "200":
+          description: "Request successful, hierarchy returned below."
           content:
             application/json:
               schema:
@@ -194,7 +194,7 @@ paths:
                     type: array
                     items:
                       $ref: ./models/api-body-schemas/CellSets.v1.yaml
-        '404':
+        "404":
           description: Experiment not found.
           content:
             application/json:
@@ -208,12 +208,12 @@ paths:
         schema:
           type: string
     put:
-      summary: ''
+      summary: ""
       operationId: updateExperimentCellSetsById
-      x-eov-operation-id: 'experiment#updateCellSets'
+      x-eov-operation-id: experiment#updateCellSets
       x-eov-operation-handler: routes/experiment
       responses:
-        '200':
+        "200":
           description: Update to object in response successful.
           content:
             application/json:
@@ -233,21 +233,21 @@ paths:
                   - $ref: ./models/api-body-schemas/CellSets.v1.yaml
       tags:
         - experiments
-  '/experiments/{experimentId}/processingConfig':
+  "/experiments/{experimentId}/processingConfig":
     get:
       summary: Retrieve processing configuration
       description: Returns a hirearchical view of processing configuration used in the experiment.
       operationId: getExperimentProcessingConfigById
-      x-eov-operation-id: 'experiment#getProcessingConfig'
+      x-eov-operation-id: experiment#getProcessingConfig
       x-eov-operation-handler: routes/experiment
       responses:
-        '200':
-          description: 'Fetch successful, response below.'
+        "200":
+          description: "Fetch successful, response below."
           content:
             application/json:
               schema:
                 $ref: ./models/ProcessingConfig.v1.yaml
-        '404':
+        "404":
           description: Experiment not found.
           content:
             application/json:
@@ -263,12 +263,12 @@ paths:
         schema:
           type: string
     put:
-      summary: ''
+      summary: ""
       operationId: updateExperimentProcessingConfigById
-      x-eov-operation-id: 'experiment#updateProcessingConfig'
+      x-eov-operation-id: experiment#updateProcessingConfig
       x-eov-operation-handler: routes/experiment
       responses:
-        '200':
+        "200":
           description: Update to object in response successful.
           content:
             application/json:
@@ -296,7 +296,7 @@ paths:
         description: Updates the keys specified by `name` with the body specified by `body`. A standard DynamoDB UpdateItem request should be called on the update.
       tags:
         - processing-config
-  '/experiments/{experimentId}/plots-tables/{plotUuid}':
+  "/experiments/{experimentId}/plots-tables/{plotUuid}":
     parameters:
       - schema:
           type: string
@@ -309,24 +309,24 @@ paths:
         in: path
         required: true
     put:
-      summary: ''
+      summary: ""
       operationId: updatePlotTable
-      x-eov-operation-id: 'plots-tables#update'
+      x-eov-operation-id: plots-tables#update
       x-eov-operation-handler: routes/plots-tables
       responses:
-        '200':
+        "200":
           description: Update to object in response successful.
           content:
             application/json:
               schema:
                 $ref: ./models/api-body-schemas/PlotTableConfig.v1.yaml
-        '201':
+        "201":
           description: New resource created.
           content:
             application/json:
               schema:
                 $ref: ./models/api-body-schemas/PlotTableConfig.v1.yaml
-        '404':
+        "404":
           description: Invalid experiment ID specified.
       description: Updates a plot and table for a given experiment with the data specified.
       requestBody:
@@ -336,28 +336,28 @@ paths:
               $ref: ./models/api-body-schemas/PlotTableConfig.v1.yaml
         description: The new configuration to update the old one by.
     get:
-      summary: ''
+      summary: ""
       operationId: getPlotTable
-      x-eov-operation-id: 'plots-tables#read'
+      x-eov-operation-id: plots-tables#read
       x-eov-operation-handler: routes/plots-tables
       responses:
-        '200':
+        "200":
           description: OK
           content:
             application/json:
               schema:
                 $ref: ./models/api-body-schemas/PlotTableConfig.v1.yaml
       description: Reads a plot and table for a given experiment with the data specified.
     delete:
-      summary: ''
+      summary: ""
       operationId: deletePlotTable
-      x-eov-operation-id: 'plots-tables#delete'
+      x-eov-operation-id: plots-tables#delete
       x-eov-operation-handler: routes/plots-tables
       responses:
-        '200':
+        "200":
           description: OK
       description: Deletes a plot and table for a given experiment with the data specified.
-  '/experiments/{experimentId}/pipelines':
+  "/experiments/{experimentId}/pipelines":
     parameters:
       - schema:
           type: string
@@ -367,10 +367,10 @@ paths:
     post:
       summary: Create a new pipeline for taks execution
       operationId: createNewPipeline
-      x-eov-operation-id: 'pipelines#create'
+      x-eov-operation-id: pipelines#create
       x-eov-operation-handler: routes/pipelines
       responses:
-        '200':
+        "200":
           description: OK
           content:
             application/json:
@@ -379,37 +379,42 @@ paths:
                 properties: {}
       description: This path will create a new pipeline that can run a state machine with different bioinformatics tasks.
     get:
-      summary: ''
+      summary: ""
       operationId: get-experiments-experimentId-pipelines
-      x-eov-operation-id: 'pipelines#get'
+      x-eov-operation-id: pipelines#get
       x-eov-operation-handler: routes/pipelines
       responses:
-        '200':
+        "200":
           description: OK
           content:
             application/json:
               schema:
                 type: object
                 properties: {}
-  '/experiments/{experimentId}/mitochondrialContent':
+  "/experiments/{experimentId}/samples":
     parameters:
       - schema:
           type: string
         name: experimentId
         in: path
         required: true
-  '/experiments/{experimentId}/doubletScores':
-    parameters:
-      - schema:
-          type: string
-        name: experimentId
-        in: path
-        required: true
-components:
-  schemas:
-    dummy:
-      title: dummy
-      type: object
-      properties:
-        id:
-          type: string
+    get:
+      summary: Your GET endpoint
+      operationId: getSamples
+      x-eov-operation-id: samples#get
+      x-eov-operation-handler: routes/samples
+      tags: []
+      responses:
+        "200":
+          description: "Fetch successful, samples returned below."
+          content:
+            application/json:
+              schema:
+                $ref: ./models/SampleResponse.v1.yaml
+        "400":
+          description: Samples not found.
+          content:
+            application/json:
+              schema:
+                $ref: ./models/HTTPError.v1.yaml
+      description: Get all samples for an experiment