Add init test experiments

api/jest.config.ts

+import type { Config } from '@jest/types';
+import * as fs from 'fs';
+import * as dotenv from 'dotenv';
+
+['.env.defaults', '.env'].forEach((f) => dotenv.config({ path: f }));
+
+const srcPath = 'src/engine/connectors';
+const engine_type = process.env.ENGINE_TYPE; // if there no engine all tests will run
+
+export default async (): Promise<Config.InitialOptions> => {
+  const dirs = (await fs.promises.readdir(srcPath))
+    .filter((dir) => dir !== engine_type)
+    .map((dir) => `${srcPath}/${dir}`);
+
+  return {
+    moduleFileExtensions: ['js', 'json', 'ts'],
+    testPathIgnorePatterns: dirs,
+    rootDir: 'src',
+    testRegex: '.*\\.spec\\.ts$',
+    transform: {
+      '^.+\\.(t|j)s$': 'ts-jest',
+    },
+    collectCoverageFrom: ['**/*.(t|j)s'],
+    coverageDirectory: '../coverage',
+    testEnvironment: 'node',
+    setupFiles: ['dotenv/config'],
+    moduleNameMapper: {
+      '^src/(.*)$': '<rootDir>/$1',
+    },
+  };
+};

api/package-lock.json

@@ -28,7 +28,7 @@
       "devDependencies": {
         "@nestjs/cli": "^8.0.0",
         "@nestjs/schematics": "^8.0.0",
-        "@nestjs/testing": "^8.0.0",
+        "@nestjs/testing": "^8.2.2",
         "@types/express": "^4.17.13",
         "@types/jest": "^27.0.1",
         "@types/node": "^16.0.0",
@@ -2084,13 +2084,13 @@
       "dev": true
     },
     "node_modules/@nestjs/testing": {
-      "version": "8.0.6",
-      "resolved": "https://registry.npmjs.org/@nestjs/testing/-/testing-8.0.6.tgz",
-      "integrity": "sha512-HRXGM5RlGa+o+kxWI9DQCALndSvL3Remjg1cZVFp2w2s5eXRPpiFMo9puXtu9DSc4tz78xYcQGmEaeYNTB7gvg==",
+      "version": "8.2.2",
+      "resolved": "https://registry.npmjs.org/@nestjs/testing/-/testing-8.2.2.tgz",
+      "integrity": "sha512-TeNdmjSMKKCw6Z4duu5h4FuGtBV0SXqM4qxLytFJ6ZobaODjqh85u9fWqJlthH+XuHslVYsmNBkCeNrgzyrL8A==",
       "dev": true,
       "dependencies": {
         "optional": "0.1.4",
-        "tslib": "2.3.0"
+        "tslib": "2.3.1"
       },
       "funding": {
         "type": "opencollective",
@@ -2111,6 +2111,12 @@
         }
       }
     },
+    "node_modules/@nestjs/testing/node_modules/tslib": {
+      "version": "2.3.1",
+      "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.3.1.tgz",
+      "integrity": "sha512-77EbyPPpMz+FRFRuAFlWMtmgUWGe9UOG2Z25NqCwiIjRhOf5iKGuzSe5P2w1laq+FkRy4p+PCuVkJSGkzTEKVw==",
+      "dev": true
+    },
     "node_modules/@nestjs/typeorm": {
       "version": "8.0.2",
       "resolved": "https://registry.npmjs.org/@nestjs/typeorm/-/typeorm-8.0.2.tgz",
@@ -12162,13 +12168,21 @@
       }
     },
     "@nestjs/testing": {
-      "version": "8.0.6",
-      "resolved": "https://registry.npmjs.org/@nestjs/testing/-/testing-8.0.6.tgz",
-      "integrity": "sha512-HRXGM5RlGa+o+kxWI9DQCALndSvL3Remjg1cZVFp2w2s5eXRPpiFMo9puXtu9DSc4tz78xYcQGmEaeYNTB7gvg==",
+      "version": "8.2.2",
+      "resolved": "https://registry.npmjs.org/@nestjs/testing/-/testing-8.2.2.tgz",
+      "integrity": "sha512-TeNdmjSMKKCw6Z4duu5h4FuGtBV0SXqM4qxLytFJ6ZobaODjqh85u9fWqJlthH+XuHslVYsmNBkCeNrgzyrL8A==",
       "dev": true,
       "requires": {
         "optional": "0.1.4",
-        "tslib": "2.3.0"
+        "tslib": "2.3.1"
+      },
+      "dependencies": {
+        "tslib": {
+          "version": "2.3.1",
+          "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.3.1.tgz",
+          "integrity": "sha512-77EbyPPpMz+FRFRuAFlWMtmgUWGe9UOG2Z25NqCwiIjRhOf5iKGuzSe5P2w1laq+FkRy4p+PCuVkJSGkzTEKVw==",
+          "dev": true
+        }
       }
     },
     "@nestjs/typeorm": {

api/package.json

@@ -18,7 +18,7 @@
     "test:watch": "jest --watch",
     "test:cov": "jest --coverage",
     "test:debug": "node --inspect-brk -r tsconfig-paths/register -r ts-node/register node_modules/.bin/jest --runInBand",
-    "test:e2e": "jest --config ./test/jest-e2e.json",
+    "test:e2e": "jest --config ./test/jest.e2e-config.ts",
     "prepare": "cd .. && husky install api/.husky"
   },
   "dependencies": {
@@ -41,7 +41,7 @@
   "devDependencies": {
     "@nestjs/cli": "^8.0.0",
     "@nestjs/schematics": "^8.0.0",
-    "@nestjs/testing": "^8.0.0",
+    "@nestjs/testing": "^8.2.2",
     "@types/express": "^4.17.13",
     "@types/jest": "^27.0.1",
     "@types/node": "^16.0.0",
@@ -60,22 +60,5 @@
     "ts-node": "^10.0.0",
     "tsconfig-paths": "^3.10.1",
     "typescript": "^4.3.5"
-  },
-  "jest": {
-    "moduleFileExtensions": [
-      "js",
-      "json",
-      "ts"
-    ],
-    "rootDir": "src",
-    "testRegex": ".*\\.spec\\.ts$",
-    "transform": {
-      "^.+\\.(t|j)s$": "ts-jest"
-    },
-    "collectCoverageFrom": [
-      "**/*.(t|j)s"
-    ],
-    "coverageDirectory": "../coverage",
-    "testEnvironment": "node"
   }
 }

api/src/engine/connectors/exareme/tests/test-utilities.ts

+import { IEngineService } from 'src/engine/engine.interfaces';
+import { Experiment } from 'src/engine/models/experiment/experiment.model';
+import { ExperimentCreateInput } from 'src/engine/models/experiment/input/experiment-create.input';
+
+const TIMEOUT_DURATION_SECONDS = 60 * 10;
+
+const TEST_PATHOLOGIES = {
+  dementia: {
+    code: 'dementia',
+    datasets: [
+      {
+        code: 'desd-synthdata',
+      },
+      { code: 'edsd' },
+      { code: 'ppmi' },
+      { code: 'fake_longitudinal' },
+    ],
+  },
+  mentalhealth: {
+    code: 'mentalhealth',
+    datasets: [{ code: 'demo' }],
+  },
+  tbi: {
+    code: 'tbi',
+    datasets: [{ code: 'dummy_tbi' }],
+  },
+};
+
+const createExperiment = async (
+  input: ExperimentCreateInput,
+  service: IEngineService,
+): Promise<Experiment | undefined> => {
+  return await service.createExperiment(input, false);
+};
+
+const waitForResult = (
+  id: string,
+  service: IEngineService,
+): Promise<Experiment> =>
+  new Promise((resolve, reject) => {
+    let elapsed = 0;
+    const timerId = setInterval(async () => {
+      const experiment = await service.getExperiment(id);
+
+      const loading = experiment ? experiment.status === 'pending' : true;
+
+      if (!loading) {
+        clearInterval(timerId);
+        resolve(experiment);
+      }
+
+      if (elapsed > TIMEOUT_DURATION_SECONDS) {
+        clearInterval(timerId);
+        reject(
+          `Query experiment ${experiment.id} timeout after ${TIMEOUT_DURATION_SECONDS} s`,
+        );
+      }
+
+      elapsed = elapsed + 0.3;
+    }, 300);
+  });
+
+const uid = (): string =>
+  'xxxxxxxx'.replace(/[xy]/g, (c) => {
+    const r = (Math.random() * 16) | 0;
+    const v = c === 'x' ? r : (r & 0x3) | 0x8;
+
+    return v.toString(16);
+  });
+
+export {
+  createExperiment,
+  uid,
+  waitForResult,
+  TEST_PATHOLOGIES,
+  TIMEOUT_DURATION_SECONDS,
+};

api/src/engine/connectors/exareme/tests/units/calibration-belt.e2e-spec.ts

+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import {
+  createExperiment,
+  TEST_PATHOLOGIES,
+  TIMEOUT_DURATION_SECONDS,
+  waitForResult,
+} from '../test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+  let exaremeService: IEngineService;
+
+  beforeEach(async () => {
+    const moduleRef: TestingModule = await Test.createTestingModule({
+      imports: [AppModule],
+    }).compile();
+
+    exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+  });
+
+  const modelSlug = `calibration-belt-${Math.round(Math.random() * 10000)}`;
+  const algorithmId = 'CALIBRATION_BELT';
+
+  const input: ExperimentCreateInput = {
+    name: modelSlug,
+    variables: ['mortality_gose'],
+    coVariables: ['mortality_core'],
+    datasets: TEST_PATHOLOGIES.tbi.datasets
+      .filter((d) => d.code !== 'fake_longitudinal')
+      .map((d) => d.code),
+    domain: TEST_PATHOLOGIES.tbi.code,
+    algorithm: {
+      id: algorithmId,
+      type: 'string',
+      parameters: [
+        {
+          id: 'devel',
+          value: ['external'],
+        },
+        {
+          id: 'max_deg',
+          value: ['4'],
+        },
+        {
+          id: 'confLevels',
+          value: ['0.80,0.95'],
+        },
+        {
+          id: 'thres',
+          value: ['0.95'],
+        },
+        {
+          id: 'num_points',
+          value: ['200'],
+        },
+      ],
+    },
+    filter: '',
+  };
+
+  describe('Integration Test for experiment API', () => {
+    it(`create ${algorithmId}`, async () => {
+      const experiment = await createExperiment(input, exaremeService);
+
+      expect(experiment).toBeTruthy();
+      expect(experiment?.status).toStrictEqual('pending');
+
+      expect(experiment?.id).toBeTruthy();
+
+      const experimentResult = await waitForResult(
+        experiment?.id ?? '',
+        exaremeService,
+      );
+
+      expect(experimentResult.status).toStrictEqual('success');
+      expect(experimentResult).toBeTruthy();
+
+      expect(experimentResult.results).toHaveLength(1);
+    });
+  });
+});

api/test/app.e2e-spec.ts

 import { Test, TestingModule } from '@nestjs/testing';
 import { INestApplication } from '@nestjs/common';
 import * as request from 'supertest';
-import { AppModule } from './../src/app.module';
+import { AppModule } from 'src/main/app.module';
 
 describe('AppController (e2e)', () => {
   let app: INestApplication;

api/test/jest-e2e.json

-{
-  "moduleFileExtensions": ["js", "json", "ts"],
-  "rootDir": ".",
-  "testEnvironment": "node",
-  "testRegex": ".e2e-spec.ts$",
-  "transform": {
-    "^.+\\.(t|j)s$": "ts-jest"
-  }
-}

api/test/jest.e2e-config.ts

+import type { Config } from '@jest/types';
+import * as fs from 'fs';
+import * as dotenv from 'dotenv';
+
+['.env.defaults', '.env'].forEach((f) => dotenv.config({ path: f }));
+
+const srcPath = 'src/engine/connectors';
+const engine_type = process.env.ENGINE_TYPE; // if there no engine all tests will run
+
+export default async (): Promise<Config.InitialOptions> => {
+  const dirs = (await fs.promises.readdir(srcPath))
+    .filter((dir) => dir !== engine_type)
+    .map((dir) => `${srcPath}/${dir}`);
+
+  return {
+    moduleFileExtensions: ['js', 'json', 'ts'],
+    testPathIgnorePatterns: dirs,
+    rootDir: '../src',
+    testRegex: '.e2e-spec.ts$',
+    transform: {
+      '^.+\\.(t|j)s$': 'ts-jest',
+    },
+    collectCoverageFrom: ['**/*.(t|j)s'],
+    coverageDirectory: '../coverage',
+    testEnvironment: 'node',
+    setupFiles: ['dotenv/config'],
+    moduleNameMapper: {
+      '^src/(.*)$': '<rootDir>/$1',
+    },
+  };
+};