diff --git a/api/jest.config.ts b/api/jest.config.ts
new file mode 100644
index 0000000000000000000000000000000000000000..09e402b93abdd342aa1ba638532a1805527a247d
--- /dev/null
+++ b/api/jest.config.ts
@@ -0,0 +1,31 @@
+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',
+ },
+ };
+};
diff --git a/api/package-lock.json b/api/package-lock.json
index 88182859b9a42510792332bff648111830b823b3..25f9900becd2762b1938002feb162fec7c2aad1b 100644
--- a/api/package-lock.json
+++ b/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": {
diff --git a/api/package.json b/api/package.json
index 1885442d70f4ac545ac7fc662ec9bef27d1d21de..9dfbc4ba56b531dc1bb627445150d9a1f8928e11 100644
--- a/api/package.json
+++ b/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"
}
}
diff --git a/api/src/engine/connectors/exareme/tests/test-utilities.ts b/api/src/engine/connectors/exareme/tests/test-utilities.ts
new file mode 100644
index 0000000000000000000000000000000000000000..116863a5dffb798ed9c6bbca23fdeeb48785c942
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/test-utilities.ts
@@ -0,0 +1,77 @@
+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 ${TIMEOUT_DURATION_SECONDS} s`,
+ );
+ }
+
+ elapsed = elapsed + 0.3;
+ }, 300);
+ });
+
+const uid = (): string =>
+ 'xxxxxxxx'.replace(/[xy]/g, (c) => {
+ const r = (Math.random() * 16) | 0;
+ const v = c === 'x' ? r : (r & 0x3) | 0x8;
+
+ return v.toString(16);
+ });
+
+export {
+ createExperiment,
+ uid,
+ waitForResult,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+};
diff --git a/api/src/engine/connectors/exareme/tests/units/calibration-belt.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/units/calibration-belt.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..34d674bd3c7877b7a91abe86bba9d1364073c7c7
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/units/calibration-belt.e2e-spec.ts
@@ -0,0 +1,86 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import {
+ createExperiment,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+
+ const modelSlug = `calibration-belt-${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 ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult.status).toStrictEqual('success');
+ expect(experimentResult).toBeTruthy();
+
+ expect(experimentResult.results).toHaveLength(1);
+ });
+ });
+});
diff --git a/api/test/app.e2e-spec.ts b/api/test/app.e2e-spec.ts
index 50cda62332e9474925e819ff946358a9c40d1bf2..92622c06ac54f7020c4be59cc4f3751feffeef0b 100644
--- a/api/test/app.e2e-spec.ts
+++ b/api/test/app.e2e-spec.ts
@@ -1,7 +1,7 @@
import { Test, TestingModule } from '@nestjs/testing';
import { INestApplication } from '@nestjs/common';
import * as request from 'supertest';
-import { AppModule } from './../src/app.module';
+import { AppModule } from 'src/main/app.module';
describe('AppController (e2e)', () => {
let app: INestApplication;
diff --git a/api/test/jest-e2e.json b/api/test/jest-e2e.json
deleted file mode 100644
index e9d912f3e3cefc18505d3cd19b3a5a9f567f5de0..0000000000000000000000000000000000000000
--- a/api/test/jest-e2e.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
- "moduleFileExtensions": ["js", "json", "ts"],
- "rootDir": ".",
- "testEnvironment": "node",
- "testRegex": ".e2e-spec.ts$",
- "transform": {
- "^.+\\.(t|j)s$": "ts-jest"
- }
-}
diff --git a/api/test/jest.e2e-config.ts b/api/test/jest.e2e-config.ts
new file mode 100644
index 0000000000000000000000000000000000000000..cad149913075e7aa049a6a11ea40b7e96b92e476
--- /dev/null
+++ b/api/test/jest.e2e-config.ts
@@ -0,0 +1,31 @@
+import type { Config } from '@jest/types';
+import * as fs from 'fs';
+import * as dotenv from 'dotenv';
+
+['.env.defaults', '.env'].forEach((f) => dotenv.config({ path: f }));
+
+const srcPath = 'src/engine/connectors';
+const engine_type = process.env.ENGINE_TYPE; // if there no engine all tests will run
+
+export default async (): Promise<Config.InitialOptions> => {
+ const dirs = (await fs.promises.readdir(srcPath))
+ .filter((dir) => dir !== engine_type)
+ .map((dir) => `${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',
+ },
+ };
+};