Merge pull request #111 from biomage-org/example-experiment-fields

[BIOMAGE-2386] Example experiment fields

src/api.v2/model/Experiment.js

@@ -67,9 +67,32 @@ class Experiment extends BasicModel {
     return result;
   }
 
-
   async getExampleExperiments() {
-    return this.getAllExperiments(constants.PUBLIC_ACCESS_ID);
+    const fields = [
+      'id',
+      'name',
+      'description',
+      'publication_title',
+      'publication_url',
+      'data_source_title',
+      'data_source_url',
+      'species',
+      'cell_count',
+    ];
+
+    const aliasedExperimentFields = fields.map((column) => `e.${column}`);
+
+    const result = await this.sql
+      .select(aliasedExperimentFields)
+      .min('s.sample_technology as sample_technology')
+      .count('s.id as sample_count') // Returns a BigInt type which is represented as string (parse?)
+      .from(tableNames.USER_ACCESS)
+      .join(`${tableNames.EXPERIMENT} as e`, 'e.id', `${tableNames.USER_ACCESS}.experiment_id`)
+      .join(`${tableNames.SAMPLE} as s`, 'e.id', 's.experiment_id')
+      .where('user_id', constants.PUBLIC_ACCESS_ID)
+      .groupBy('e.id');
+
+    return result;
   }
 
   async getExperimentData(experimentId) {

src/specs/api.v2.yaml

@@ -301,7 +301,7 @@ paths:
           content:
             application/json:
               schema:
-                $ref: "#/components/schemas/ExperimentsList"
+                $ref: "#/components/schemas/ExampleExperimentsList"
         "400":
           description: Bad Request
           content:
@@ -681,7 +681,6 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/HTTPError"
-
   "/experiments/{experimentId}/samples/{sampleId}":
     patch:
       summary: Patch sample
@@ -2150,6 +2149,8 @@ components:
       $ref: ./models/experiment-bodies/ProcessingConfig.v2.yaml
     ExperimentsList:
       $ref: ./models/experiment-bodies/ExperimentsList.v2.yaml
+    ExampleExperimentsList:
+      $ref: ./models/experiment-bodies/ExampleExperimentsList.v2.yaml
     CreateSamples:
       $ref: ./models/samples-bodies/CreateSamples.v2.yaml
     GetSamples:

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

@@ -0,0 +1,52 @@
+title: Get all example experiments
+type: array
+items:
+  type: object
+  properties:
+    id:
+      type: string
+    name:
+      type: string
+    description:
+      type: string
+      nullable: true
+    publicationTitle:
+      type: string
+      nullable: true
+    publicationUrl:
+      type: string
+      nullable: true
+    dataSourceTitle:
+      type: string
+      nullable: true
+    dataSourceUrl:
+      type: string
+      nullable: true
+    species:
+      type: string
+      nullable: true
+    cellCount:
+      type: string
+      nullable: true
+    sampleCount:
+      type: string
+    sampleTechnology:
+      type: string
+      nullable: true
+
+  required:
+    - id
+    - name
+    - description
+    - publicationTitle
+    - publicationUrl
+    - dataSourceTitle
+    - dataSourceUrl
+    - species
+    - cellCount
+    - sampleCount
+    - sampleTechnology
+
+  additionalProperties: false
+
+additionalProperties: false

src/sql/migrations/20230207141717_add_example_experiment_fields.js

@@ -0,0 +1,29 @@
+/**
+ * @param { import("knex").Knex } knex
+ * @returns { Promise<void> }
+ */
+exports.up = async (knex) => {
+  await knex.schema.alterTable('experiment', (table) => {
+    table.string('publication_title').nullable();
+    table.string('publication_url').nullable();
+    table.string('data_source_title').nullable();
+    table.string('data_source_url').nullable();
+    table.string('species').nullable();
+    table.integer('cell_count').nullable();
+  });
+};
+
+/**
+ * @param { import("knex").Knex } knex
+ * @returns { Promise<void> }
+ */
+exports.down = async (knex) => {
+  await knex.schema.alterTable('experiment', (table) => {
+    table.dropColumn('publication_title');
+    table.dropColumn('publication_url');
+    table.dropColumn('data_source_title');
+    table.dropColumn('data_source_url');
+    table.dropColumn('species');
+    table.dropColumn('cell_count');
+  });
+};

tests/api.v2/mocks/getMockSqlClient.js

@@ -27,6 +27,8 @@ module.exports = () => {
     onConflict: jest.fn().mockReturnThis(),
     merge: jest.fn().mockReturnThis(),
     andWhereLike: jest.fn().mockReturnThis(),
+    min: jest.fn().mockReturnThis(),
+    count: jest.fn().mockReturnThis(),
     ref: jest.fn(),
   };
 

tests/api.v2/model/Experiment.test.js

@@ -32,6 +32,7 @@ jest.mock('../../../src/sql/helpers', () => ({
 
 const Experiment = require('../../../src/api.v2/model/Experiment');
 const constants = require('../../../src/utils/constants');
+const tableNames = require('../../../src/api.v2/model/tableNames');
 
 const mockExperimentId = 'mockExperimentId';
 const mockSampleId = 'mockSampleId';
@@ -77,15 +78,35 @@ describe('model/Experiment', () => {
   });
 
   it('getExampleExperiments works correctly', async () => {
-    const expectedResult = { isMockResult: true };
+    const queryResult = 'result';
+
+    mockSqlClient.groupBy.mockReturnValueOnce(queryResult);
 
-    const getAllExperimentsSpy = jest.spyOn(Experiment.prototype, 'getAllExperiments')
-      .mockImplementationOnce(() => Promise.resolve(expectedResult));
+    const expectedResult = await new Experiment().getExampleExperiments();
 
-    const result = await new Experiment().getExampleExperiments('mockUserId');
+    expect(queryResult).toEqual(expectedResult);
 
-    expect(result).toBe(expectedResult);
-    expect(getAllExperimentsSpy).toHaveBeenCalledWith(constants.PUBLIC_ACCESS_ID);
+    expect(sqlClient.get).toHaveBeenCalled();
+    expect(mockSqlClient.select).toHaveBeenCalledWith(
+      [
+        'e.id',
+        'e.name',
+        'e.description',
+        'e.publication_title',
+        'e.publication_url',
+        'e.data_source_title',
+        'e.data_source_url',
+        'e.species',
+        'e.cell_count',
+      ],
+    );
+    expect(mockSqlClient.min).toHaveBeenCalledWith('s.sample_technology as sample_technology');
+    expect(mockSqlClient.count).toHaveBeenCalledWith('s.id as sample_count');
+    expect(mockSqlClient.from).toHaveBeenCalledWith(tableNames.USER_ACCESS);
+    expect(mockSqlClient.join).toHaveBeenCalledWith(`${tableNames.EXPERIMENT} as e`, 'e.id', `${tableNames.USER_ACCESS}.experiment_id`);
+    expect(mockSqlClient.join).toHaveBeenCalledWith(`${tableNames.SAMPLE} as s`, 'e.id', 's.experiment_id');
+    expect(mockSqlClient.where).toHaveBeenCalledWith('user_id', constants.PUBLIC_ACCESS_ID);
+    expect(mockSqlClient.groupBy).toHaveBeenCalledWith('e.id');
   });
 
   it('getExperimentData works correctly', async () => {