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 e63192102b420fdb76d7313c66d3a464c0b52564..1f8f383b2a49e4d369a5a5447253a42e221e5e01 100644
--- a/api/package-lock.json
+++ b/api/package-lock.json
@@ -29,7 +29,7 @@
"@eclass/semantic-release-docker": "^2.0.0",
"@nestjs/cli": "^8.0.0",
"@nestjs/schematics": "^8.0.0",
- "@nestjs/testing": "^8.0.0",
+ "@nestjs/testing": "^8.2.2",
"@semantic-release/changelog": "^6.0.1",
"@semantic-release/git": "^10.0.1",
"@semantic-release/gitlab": "^7.0.4",
@@ -54,22 +54,30 @@
}
},
"node_modules/@angular-devkit/core": {
- "version": "12.1.4",
- "resolved": "https://registry.npmjs.org/@angular-devkit/core/-/core-12.1.4.tgz",
- "integrity": "sha512-KOzGD8JbP/7EeUwPiU5x+fo3ZEQ5R4IVW5WoH92PaO3mdpqXC7UL2MWLct8PUe9il9nqJMvrBMldSSvP9PCT2w==",
+ "version": "13.1.2",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/core/-/core-13.1.2.tgz",
+ "integrity": "sha512-uXVesIRiCL/Nv+RSV8JM4j8IoZiGCGnqV2FOJ1hvH7DPxIjhjPMdG/B54xMydZpeASW3ofuxeORyAXxFIBm8Zg==",
"dev": true,
"dependencies": {
- "ajv": "8.6.0",
- "ajv-formats": "2.1.0",
+ "ajv": "8.8.2",
+ "ajv-formats": "2.1.1",
"fast-json-stable-stringify": "2.1.0",
"magic-string": "0.25.7",
"rxjs": "6.6.7",
"source-map": "0.7.3"
},
"engines": {
- "node": "^12.14.1 || >=14.0.0",
- "npm": "^6.11.0 || ^7.5.6",
+ "node": "^12.20.0 || ^14.15.0 || >=16.10.0",
+ "npm": "^6.11.0 || ^7.5.6 || >=8.0.0",
"yarn": ">= 1.13.0"
+ },
+ "peerDependencies": {
+ "chokidar": "^3.5.2"
+ },
+ "peerDependenciesMeta": {
+ "chokidar": {
+ "optional": true
+ }
}
},
"node_modules/@angular-devkit/core/node_modules/rxjs": {
@@ -91,31 +99,33 @@
"dev": true
},
"node_modules/@angular-devkit/schematics": {
- "version": "12.1.4",
- "resolved": "https://registry.npmjs.org/@angular-devkit/schematics/-/schematics-12.1.4.tgz",
- "integrity": "sha512-yD3y3pK/K5piOgvALFoCCiPp4H8emNa3yZL+vlpEpewVLpF1MM55LeTxc0PI5s0uqtOGVnvcbA5wYgMm3YsUEA==",
+ "version": "13.1.2",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/schematics/-/schematics-13.1.2.tgz",
+ "integrity": "sha512-ayYbHGU8QpMGx8ZyhKOBupz+Zfv/2H1pNQErahYV3qg7hA9hfjTGmNmDQ4iw0fiT04NajjUxuomlKsCsg7oXDw==",
"dev": true,
"dependencies": {
- "@angular-devkit/core": "12.1.4",
+ "@angular-devkit/core": "13.1.2",
+ "jsonc-parser": "3.0.0",
+ "magic-string": "0.25.7",
"ora": "5.4.1",
"rxjs": "6.6.7"
},
"engines": {
- "node": "^12.14.1 || >=14.0.0",
- "npm": "^6.11.0 || ^7.5.6",
+ "node": "^12.20.0 || ^14.15.0 || >=16.10.0",
+ "npm": "^6.11.0 || ^7.5.6 || >=8.0.0",
"yarn": ">= 1.13.0"
}
},
"node_modules/@angular-devkit/schematics-cli": {
- "version": "12.1.4",
- "resolved": "https://registry.npmjs.org/@angular-devkit/schematics-cli/-/schematics-cli-12.1.4.tgz",
- "integrity": "sha512-BJiyZu7TaOJUnH4XH4OKz1LjW1364BLAhpwCBAueu11YkI7hghlsx/ogvvd5RYX9JmQL70iVOVkBsoYA7XVreg==",
+ "version": "13.1.2",
+ "resolved": "https://registry.npmjs.org/@angular-devkit/schematics-cli/-/schematics-cli-13.1.2.tgz",
+ "integrity": "sha512-XSkcVuaaajijQOWE8YerY/8DVuYQWvXxVukweEwkaHSftDQZhfCOZ83nGKbuWkdOdnuDbrc9ve5ZzekplkzVQw==",
"dev": true,
"dependencies": {
- "@angular-devkit/core": "12.1.4",
- "@angular-devkit/schematics": "12.1.4",
+ "@angular-devkit/core": "13.1.2",
+ "@angular-devkit/schematics": "13.1.2",
"ansi-colors": "4.1.1",
- "inquirer": "8.1.1",
+ "inquirer": "8.2.0",
"minimist": "1.2.5",
"symbol-observable": "4.0.0"
},
@@ -123,8 +133,8 @@
"schematics": "bin/schematics.js"
},
"engines": {
- "node": "^12.14.1 || >=14.0.0",
- "npm": "^6.11.0 || ^7.5.6",
+ "node": "^12.20.0 || ^14.15.0 || >=16.10.0",
+ "npm": "^6.11.0 || ^7.5.6 || >=8.0.0",
"yarn": ">= 1.13.0"
}
},
@@ -145,9 +155,9 @@
}
},
"node_modules/@angular-devkit/schematics-cli/node_modules/inquirer": {
- "version": "8.1.1",
- "resolved": "https://registry.npmjs.org/inquirer/-/inquirer-8.1.1.tgz",
- "integrity": "sha512-hUDjc3vBkh/uk1gPfMAD/7Z188Q8cvTGl0nxwaCdwSbzFh6ZKkZh+s2ozVxbE5G9ZNRyeY0+lgbAIOUFsFf98w==",
+ "version": "8.2.0",
+ "resolved": "https://registry.npmjs.org/inquirer/-/inquirer-8.2.0.tgz",
+ "integrity": "sha512-0crLweprevJ02tTuA6ThpoAERAGyVILC4sS74uib58Xf/zSr1/ZWtmm7D5CI+bSQEaA04f0K7idaHpQbSWgiVQ==",
"dev": true,
"dependencies": {
"ansi-escapes": "^4.2.1",
@@ -158,9 +168,9 @@
"figures": "^3.0.0",
"lodash": "^4.17.21",
"mute-stream": "0.0.8",
- "ora": "^5.3.0",
+ "ora": "^5.4.1",
"run-async": "^2.4.0",
- "rxjs": "^6.6.6",
+ "rxjs": "^7.2.0",
"string-width": "^4.1.0",
"strip-ansi": "^6.0.0",
"through": "^2.3.6"
@@ -169,47 +179,6 @@
"node": ">=8.0.0"
}
},
- "node_modules/@angular-devkit/schematics-cli/node_modules/is-fullwidth-code-point": {
- "version": "3.0.0",
- "resolved": "https://registry.npmjs.org/is-fullwidth-code-point/-/is-fullwidth-code-point-3.0.0.tgz",
- "integrity": "sha512-zymm5+u+sCsSWyD9qNaejV3DFvhCKclKdizYaJUuHA83RLjb7nSuGnddCHGv0hk+KY7BMAlsWeK4Ueg6EV6XQg==",
- "dev": true,
- "engines": {
- "node": ">=8"
- }
- },
- "node_modules/@angular-devkit/schematics-cli/node_modules/rxjs": {
- "version": "6.6.7",
- "resolved": "https://registry.npmjs.org/rxjs/-/rxjs-6.6.7.tgz",
- "integrity": "sha512-hTdwr+7yYNIT5n4AMYp85KA6yw2Va0FLa3Rguvbpa4W3I5xynaBZo41cM3XM+4Q6fRMj3sBYIR1VAmZMXYJvRQ==",
- "dev": true,
- "dependencies": {
- "tslib": "^1.9.0"
- },
- "engines": {
- "npm": ">=2.0.0"
- }
- },
- "node_modules/@angular-devkit/schematics-cli/node_modules/string-width": {
- "version": "4.2.2",
- "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.2.tgz",
- "integrity": "sha512-XBJbT3N4JhVumXE0eoLU9DCjcaF92KLNqTmFCnG1pf8duUxFGwtP6AD6nkjw9a3IdiRtL3E2w3JDiE/xi3vOeA==",
- "dev": true,
- "dependencies": {
- "emoji-regex": "^8.0.0",
- "is-fullwidth-code-point": "^3.0.0",
- "strip-ansi": "^6.0.0"
- },
- "engines": {
- "node": ">=8"
- }
- },
- "node_modules/@angular-devkit/schematics-cli/node_modules/tslib": {
- "version": "1.14.1",
- "resolved": "https://registry.npmjs.org/tslib/-/tslib-1.14.1.tgz",
- "integrity": "sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg==",
- "dev": true
- },
"node_modules/@angular-devkit/schematics/node_modules/rxjs": {
"version": "6.6.7",
"resolved": "https://registry.npmjs.org/rxjs/-/rxjs-6.6.7.tgz",
@@ -259,9 +228,9 @@
"integrity": "sha512-F0KIgDJfy2nA3zMLmWGKxcH2ZVEtCZXHHdOQs2gSaQ27+lNeEfGxzkIw90aXswATX7AZ33tahPbzy6KAfUreVw=="
},
"node_modules/@apollographql/apollo-tools": {
- "version": "0.5.1",
- "resolved": "https://registry.npmjs.org/@apollographql/apollo-tools/-/apollo-tools-0.5.1.tgz",
- "integrity": "sha512-ZII+/xUFfb9ezDU2gad114+zScxVFMVlZ91f8fGApMzlS1kkqoyLnC4AJaQ1Ya/X+b63I20B4Gd+eCL8QuB4sA==",
+ "version": "0.5.2",
+ "resolved": "https://registry.npmjs.org/@apollographql/apollo-tools/-/apollo-tools-0.5.2.tgz",
+ "integrity": "sha512-KxZiw0Us3k1d0YkJDhOpVH5rJ+mBfjXcgoRoCcslbgirjgLotKMzOcx4PZ7YTEvvEROmvG7X3Aon41GvMmyGsw==",
"engines": {
"node": ">=8",
"npm": ">=6"
@@ -301,29 +270,29 @@
}
},
"node_modules/@babel/compat-data": {
- "version": "7.15.0",
- "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.15.0.tgz",
- "integrity": "sha512-0NqAC1IJE0S0+lL1SWFMxMkz1pKCNCjI4tr2Zx4LJSXxCLAdr6KyArnY+sno5m3yH9g737ygOyPABDsnXkpxiA==",
+ "version": "7.16.8",
+ "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.16.8.tgz",
+ "integrity": "sha512-m7OkX0IdKLKPpBlJtF561YJal5y/jyI5fNfWbPxh2D/nbzzGI4qRyrD8xO2jB24u7l+5I2a43scCG2IrfjC50Q==",
"dev": true,
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/core": {
- "version": "7.15.5",
- "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.15.5.tgz",
- "integrity": "sha512-pYgXxiwAgQpgM1bNkZsDEq85f0ggXMA5L7c+o3tskGMh2BunCI9QUwB9Z4jpvXUOuMdyGKiGKQiRe11VS6Jzvg==",
- "dev": true,
- "dependencies": {
- "@babel/code-frame": "^7.14.5",
- "@babel/generator": "^7.15.4",
- "@babel/helper-compilation-targets": "^7.15.4",
- "@babel/helper-module-transforms": "^7.15.4",
- "@babel/helpers": "^7.15.4",
- "@babel/parser": "^7.15.5",
- "@babel/template": "^7.15.4",
- "@babel/traverse": "^7.15.4",
- "@babel/types": "^7.15.4",
+ "version": "7.16.12",
+ "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.16.12.tgz",
+ "integrity": "sha512-dK5PtG1uiN2ikk++5OzSYsitZKny4wOCD0nrO4TqnW4BVBTQ2NGS3NgilvT/TEyxTST7LNyWV/T4tXDoD3fOgg==",
+ "dev": true,
+ "dependencies": {
+ "@babel/code-frame": "^7.16.7",
+ "@babel/generator": "^7.16.8",
+ "@babel/helper-compilation-targets": "^7.16.7",
+ "@babel/helper-module-transforms": "^7.16.7",
+ "@babel/helpers": "^7.16.7",
+ "@babel/parser": "^7.16.12",
+ "@babel/template": "^7.16.7",
+ "@babel/traverse": "^7.16.10",
+ "@babel/types": "^7.16.8",
"convert-source-map": "^1.7.0",
"debug": "^4.1.0",
"gensync": "^1.0.0-beta.2",
@@ -340,12 +309,12 @@
}
},
"node_modules/@babel/core/node_modules/@babel/code-frame": {
- "version": "7.14.5",
- "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.14.5.tgz",
- "integrity": "sha512-9pzDqyc6OLDaqe+zbACgFkb6fKMNG6CObKpnYXChRsvYGyEdc7CA2BaqeOM+vOtCS5ndmJicPJhKAwYRI6UfFw==",
+ "version": "7.16.7",
+ "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.16.7.tgz",
+ "integrity": "sha512-iAXqUn8IIeBTNd72xsFlgaXHkMBMt6y4HJp1tIaK465CWLT/fG1aqB7ykr95gHHmlBdGbFeWWfyB4NJJ0nmeIg==",
"dev": true,
"dependencies": {
- "@babel/highlight": "^7.14.5"
+ "@babel/highlight": "^7.16.7"
},
"engines": {
"node": ">=6.9.0"
@@ -370,12 +339,12 @@
}
},
"node_modules/@babel/generator": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.15.4.tgz",
- "integrity": "sha512-d3itta0tu+UayjEORPNz6e1T3FtvWlP5N4V5M+lhp/CxT4oAA7/NcScnpRyspUMLK6tu9MNHmQHxRykuN2R7hw==",
+ "version": "7.16.8",
+ "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.16.8.tgz",
+ "integrity": "sha512-1ojZwE9+lOXzcWdWmO6TbUzDfqLD39CmEhN8+2cX9XkDo5yW1OpgfejfliysR2AWLpMamTiOiAp/mtroaymhpw==",
"dev": true,
"dependencies": {
- "@babel/types": "^7.15.4",
+ "@babel/types": "^7.16.8",
"jsesc": "^2.5.1",
"source-map": "^0.5.0"
},
@@ -393,14 +362,14 @@
}
},
"node_modules/@babel/helper-compilation-targets": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.15.4.tgz",
- "integrity": "sha512-rMWPCirulnPSe4d+gwdWXLfAXTTBj8M3guAf5xFQJ0nvFY7tfNAFnWdqaHegHlgDZOCT4qvhF3BYlSJag8yhqQ==",
+ "version": "7.16.7",
+ "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.16.7.tgz",
+ "integrity": "sha512-mGojBwIWcwGD6rfqgRXVlVYmPAv7eOpIemUG3dGnDdCY4Pae70ROij3XmfrH6Fa1h1aiDylpglbZyktfzyo/hA==",
"dev": true,
"dependencies": {
- "@babel/compat-data": "^7.15.0",
- "@babel/helper-validator-option": "^7.14.5",
- "browserslist": "^4.16.6",
+ "@babel/compat-data": "^7.16.4",
+ "@babel/helper-validator-option": "^7.16.7",
+ "browserslist": "^4.17.5",
"semver": "^6.3.0"
},
"engines": {
@@ -419,186 +388,159 @@
"semver": "bin/semver.js"
}
},
- "node_modules/@babel/helper-function-name": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-function-name/-/helper-function-name-7.15.4.tgz",
- "integrity": "sha512-Z91cOMM4DseLIGOnog+Z8OI6YseR9bua+HpvLAQ2XayUGU+neTtX+97caALaLdyu53I/fjhbeCnWnRH1O3jFOw==",
+ "node_modules/@babel/helper-environment-visitor": {
+ "version": "7.16.7",
+ "resolved": "https://registry.npmjs.org/@babel/helper-environment-visitor/-/helper-environment-visitor-7.16.7.tgz",
+ "integrity": "sha512-SLLb0AAn6PkUeAfKJCCOl9e1R53pQlGAfc4y4XuMRZfqeMYLE0dM1LMhqbGAlGQY0lfw5/ohoYWAe9V1yibRag==",
"dev": true,
"dependencies": {
- "@babel/helper-get-function-arity": "^7.15.4",
- "@babel/template": "^7.15.4",
- "@babel/types": "^7.15.4"
+ "@babel/types": "^7.16.7"
},
"engines": {
"node": ">=6.9.0"
}
},
- "node_modules/@babel/helper-get-function-arity": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-get-function-arity/-/helper-get-function-arity-7.15.4.tgz",
- "integrity": "sha512-1/AlxSF92CmGZzHnC515hm4SirTxtpDnLEJ0UyEMgTMZN+6bxXKg04dKhiRx5Enel+SUA1G1t5Ed/yQia0efrA==",
+ "node_modules/@babel/helper-function-name": {
+ "version": "7.16.7",
+ "resolved": "https://registry.npmjs.org/@babel/helper-function-name/-/helper-function-name-7.16.7.tgz",
+ "integrity": "sha512-QfDfEnIUyyBSR3HtrtGECuZ6DAyCkYFp7GHl75vFtTnn6pjKeK0T1DB5lLkFvBea8MdaiUABx3osbgLyInoejA==",
"dev": true,
"dependencies": {
- "@babel/types": "^7.15.4"
+ "@babel/helper-get-function-arity": "^7.16.7",
+ "@babel/template": "^7.16.7",
+ "@babel/types": "^7.16.7"
},
"engines": {
"node": ">=6.9.0"
}
},
- "node_modules/@babel/helper-hoist-variables": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-hoist-variables/-/helper-hoist-variables-7.15.4.tgz",
- "integrity": "sha512-VTy085egb3jUGVK9ycIxQiPbquesq0HUQ+tPO0uv5mPEBZipk+5FkRKiWq5apuyTE9FUrjENB0rCf8y+n+UuhA==",
+ "node_modules/@babel/helper-get-function-arity": {
+ "version": "7.16.7",
+ "resolved": "https://registry.npmjs.org/@babel/helper-get-function-arity/-/helper-get-function-arity-7.16.7.tgz",
+ "integrity": "sha512-flc+RLSOBXzNzVhcLu6ujeHUrD6tANAOU5ojrRx/as+tbzf8+stUCj7+IfRRoAbEZqj/ahXEMsjhOhgeZsrnTw==",
"dev": true,
"dependencies": {
- "@babel/types": "^7.15.4"
+ "@babel/types": "^7.16.7"
},
"engines": {
"node": ">=6.9.0"
}
},
- "node_modules/@babel/helper-member-expression-to-functions": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-member-expression-to-functions/-/helper-member-expression-to-functions-7.15.4.tgz",
- "integrity": "sha512-cokOMkxC/BTyNP1AlY25HuBWM32iCEsLPI4BHDpJCHHm1FU2E7dKWWIXJgQgSFiu4lp8q3bL1BIKwqkSUviqtA==",
+ "node_modules/@babel/helper-hoist-variables": {
+ "version": "7.16.7",
+ "resolved": "https://registry.npmjs.org/@babel/helper-hoist-variables/-/helper-hoist-variables-7.16.7.tgz",
+ "integrity": "sha512-m04d/0Op34H5v7pbZw6pSKP7weA6lsMvfiIAMeIvkY/R4xQtBSMFEigu9QTZ2qB/9l22vsxtM8a+Q8CzD255fg==",
"dev": true,
"dependencies": {
- "@babel/types": "^7.15.4"
+ "@babel/types": "^7.16.7"
},
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/helper-module-imports": {
- "version": "7.15.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-module-imports/-/helper-module-imports-7.15.4.tgz",
- "integrity": "sha512-jeAHZbzUwdW/xHgHQ3QmWR4Jg6j15q4w/gCfwZvtqOxoo5DKtLHk8Bsf4c5RZRC7NmLEs+ohkdq8jFefuvIxAA==",
+ "version": "7.16.7",
+ "resolved": "https://registry.npmjs.org/@babel/helper-module-imports/-/helper-module-imports-7.16.7.tgz",
+ "integrity": "sha512-LVtS6TqjJHFc+nYeITRo6VLXve70xmq7wPhWTqDJusJEgGmkAACWwMiTNrvfoQo6hEhFwAIixNkvB0jPXDL8Wg==",
"dev": true,
"dependencies": {
- "@babel/types": "^7.15.4"
+ "@babel/types": "^7.16.7"
},
"engines": {
"node": ">=6.9.0"
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@@ -1396,9 +1348,9 @@
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@@ -1419,13 +1371,13 @@
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@@ -1500,9 +1452,9 @@
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@@ -1549,33 +1501,41 @@
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+ "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.1.tgz",
+ "integrity": "sha512-dKQiRHxGD9PPRIUNIWvZhPTPpl1rf/OxTYKsqKUDjBwYylTvV7SjSHJb9ratfyzM6wCdLCOYLzs73qpg5c4iGA==",
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@@ -1587,9 +1547,9 @@
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"dev": true,
"bin": {
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@@ -1598,6 +1558,15 @@
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}
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+ "resolved": "https://registry.npmjs.org/acorn-import-assertions/-/acorn-import-assertions-1.8.0.tgz",
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@@ -1647,48 +1616,19 @@
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@@ -1893,6 +1820,9 @@
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@@ -1907,31 +1837,6 @@
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@@ -3698,23 +3496,23 @@
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@@ -3723,48 +3521,48 @@
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- "@types/express-serve-static-core": "4.17.24",
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@@ -3774,37 +3572,37 @@
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@@ -3874,6 +3672,12 @@
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@@ -3916,24 +3720,24 @@
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@@ -4797,6 +4545,11 @@
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@@ -7989,47 +7730,47 @@
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+ "resolved": "https://registry.npmjs.org/jest-jasmine2/-/jest-jasmine2-27.4.6.tgz",
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"co": "^4.6.0",
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- "jest-runtime": "^27.1.1",
- "jest-snapshot": "^27.1.1",
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+ "jest-runtime": "^27.4.6",
+ "jest-snapshot": "^27.4.6",
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@@ -8086,28 +7826,28 @@
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+ "version": "27.4.6",
+ "resolved": "https://registry.npmjs.org/jest-leak-detector/-/jest-leak-detector-27.4.6.tgz",
+ "integrity": "sha512-kkaGixDf9R7CjHm2pOzfTxZTQQQ2gHTIWKY/JZSiYTc90bZp8kSZnUMS3uLAfwTZwc0tcMRoEX74e14LG1WapA==",
"dev": true,
"dependencies": {
- "jest-get-type": "^27.0.6",
- "pretty-format": "^27.1.1"
+ "jest-get-type": "^27.4.0",
+ "pretty-format": "^27.4.6"
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+ "version": "27.4.6",
+ "resolved": "https://registry.npmjs.org/jest-matcher-utils/-/jest-matcher-utils-27.4.6.tgz",
+ "integrity": "sha512-XD4PKT3Wn1LQnRAq7ZsTI0VRuEc9OrCPFiO1XL7bftTGmfNF0DcEwMHRgqiu7NGf8ZoZDREpGrCniDkjt79WbA==",
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"chalk": "^4.0.0",
- "jest-diff": "^27.1.1",
- "jest-get-type": "^27.0.6",
- "pretty-format": "^27.1.1"
+ "jest-diff": "^27.4.6",
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+ "pretty-format": "^27.4.6"
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@@ -8130,18 +7870,18 @@
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+ "version": "27.4.6",
+ "resolved": "https://registry.npmjs.org/jest-message-util/-/jest-message-util-27.4.6.tgz",
+ "integrity": "sha512-0p5szriFU0U74czRSFjH6RyS7UYIAkn/ntwMuOwTGWrQIOh5NzXXrq72LOqIkJKKvFbPq+byZKuBz78fjBERBA==",
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"dependencies": {
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- "@jest/types": "^27.1.1",
+ "@jest/types": "^27.4.2",
"@types/stack-utils": "^2.0.0",
"chalk": "^4.0.0",
"graceful-fs": "^4.2.4",
"micromatch": "^4.0.4",
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},
@@ -8150,12 +7890,12 @@
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- "integrity": "sha512-9pzDqyc6OLDaqe+zbACgFkb6fKMNG6CObKpnYXChRsvYGyEdc7CA2BaqeOM+vOtCS5ndmJicPJhKAwYRI6UfFw==",
+ "version": "7.16.7",
+ "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.16.7.tgz",
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"dev": true,
"dependencies": {
- "@babel/highlight": "^7.14.5"
+ "@babel/highlight": "^7.16.7"
},
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@@ -8178,12 +7918,12 @@
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+ "version": "27.4.6",
+ "resolved": "https://registry.npmjs.org/jest-mock/-/jest-mock-27.4.6.tgz",
+ "integrity": "sha512-kvojdYRkst8iVSZ1EJ+vc1RRD9llueBjKzXzeCytH3dMM7zvPV/ULcfI2nr0v0VUgm3Bjt3hBCQvOeaBz+ZTHw==",
"dev": true,
"dependencies": {
- "@jest/types": "^27.1.1",
+ "@jest/types": "^27.4.2",
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},
"engines": {
@@ -8208,29 +7948,29 @@
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+ "version": "27.4.0",
+ "resolved": "https://registry.npmjs.org/jest-regex-util/-/jest-regex-util-27.4.0.tgz",
+ "integrity": "sha512-WeCpMpNnqJYMQoOjm1nTtsgbR4XHAk1u00qDoNBQoykM280+/TmgA5Qh5giC1ecy6a5d4hbSsHzpBtu5yvlbEg==",
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+ "version": "27.4.6",
+ "resolved": "https://registry.npmjs.org/jest-resolve/-/jest-resolve-27.4.6.tgz",
+ "integrity": "sha512-SFfITVApqtirbITKFAO7jOVN45UgFzcRdQanOFzjnbd+CACDoyeX7206JyU92l4cRr73+Qy/TlW51+4vHGt+zw==",
"dev": true,
"dependencies": {
- "@jest/types": "^27.1.1",
+ "@jest/types": "^27.4.2",
"chalk": "^4.0.0",
- "escalade": "^3.1.1",
"graceful-fs": "^4.2.4",
- "jest-haste-map": "^27.1.1",
+ "jest-haste-map": "^27.4.6",
"jest-pnp-resolver": "^1.2.2",
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- "jest-validate": "^27.1.1",
+ "jest-util": "^27.4.2",
+ "jest-validate": "^27.4.6",
"resolve": "^1.20.0",
+ "resolve.exports": "^1.1.0",
"slash": "^3.0.0"
},
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@@ -8238,14 +7978,14 @@
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+ "version": "27.4.6",
+ "resolved": "https://registry.npmjs.org/jest-resolve-dependencies/-/jest-resolve-dependencies-27.4.6.tgz",
+ "integrity": "sha512-W85uJZcFXEVZ7+MZqIPCscdjuctruNGXUZ3OHSXOfXR9ITgbUKeHj+uGcies+0SsvI5GtUfTw4dY7u9qjTvQOw==",
"dev": true,
"dependencies": {
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- "jest-regex-util": "^27.0.6",
- "jest-snapshot": "^27.1.1"
+ "@jest/types": "^27.4.2",
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@@ -8268,31 +8008,31 @@
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+ "resolved": "https://registry.npmjs.org/jest-runner/-/jest-runner-27.4.6.tgz",
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"exit": "^0.1.2",
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- "jest-runtime": "^27.1.1",
- "jest-util": "^27.1.1",
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"throat": "^6.0.1"
},
@@ -8317,38 +8057,33 @@
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- "@jest/test-result": "^27.1.1",
- "@jest/transform": "^27.1.1",
- "@jest/types": "^27.1.1",
- "@types/yargs": "^16.0.0",
+ "version": "27.4.6",
+ "resolved": "https://registry.npmjs.org/jest-runtime/-/jest-runtime-27.4.6.tgz",
+ "integrity": "sha512-eXYeoR/MbIpVDrjqy5d6cGCFOYBFFDeKaNWqTp0h6E74dK0zLHzASQXJpl5a2/40euBmKnprNLJ0Kh0LCndnWQ==",
+ "dev": true,
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- "jest-snapshot": "^27.1.1",
- "jest-util": "^27.1.1",
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+ "strip-bom": "^4.0.0"
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@@ -8371,9 +8106,9 @@
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@@ -15186,6 +14765,20 @@
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+ "optional": true,
+ "peer": true,
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"resolved": "https://registry.npmjs.org/json-schema-traverse/-/json-schema-traverse-0.4.1.tgz",
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+ "integrity": "sha512-AMmF99DMfEDiRJfxfY5jj5wNH/bYO09cniSqhfoyxc8sFoYIgkJy86G04UoZU5VjlpnplVu0K6Tx6E9b5+DlHA==",
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+ }
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@@ -15338,52 +14950,6 @@
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- "url": "https://github.com/sponsors/feross"
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@@ -15423,9 +14989,9 @@
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+ "version": "1.0.1",
+ "resolved": "https://registry.npmjs.org/toidentifier/-/toidentifier-1.0.1.tgz",
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@@ -15492,16 +15058,16 @@
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+ "version": "27.1.3",
+ "resolved": "https://registry.npmjs.org/ts-jest/-/ts-jest-27.1.3.tgz",
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"fast-json-stable-stringify": "2.x",
"jest-util": "^27.0.0",
"json5": "2.x",
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@@ -15516,6 +15082,7 @@
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"babel-jest": ">=27.0.0 <28",
+ "esbuild": "~0.14.0",
"jest": "^27.0.0",
"typescript": ">=3.8 <5.0"
},
@@ -15528,13 +15095,16 @@
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"dev": true,
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@@ -15567,12 +15137,12 @@
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"dev": true,
"dependencies": {
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@@ -15592,9 +15162,6 @@
"ts-node-transpile-only": "dist/bin-transpile.js",
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@@ -15611,9 +15178,9 @@
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+ "version": "8.7.0",
+ "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.7.0.tgz",
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"dev": true,
"bin": {
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@@ -15632,9 +15199,9 @@
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+ "resolved": "https://registry.npmjs.org/tapable/-/tapable-2.2.1.tgz",
+ "integrity": "sha512-GNzQvQTOIP6RyTfE2Qxb8ZVlNmw0n88vp1szwWRimP02mnTsx3Wtn5qRdqY9w2XduFNUgvOwhNnQsjwCp+kqaQ==",
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@@ -18094,14 +17475,15 @@
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- "enhanced-resolve": "^5.8.0",
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@@ -18109,71 +17491,62 @@
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"fast-glob": "3.2.7",
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"normalize-path": "3.0.0",
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"cors": "2.8.5",
- "express": "4.17.1",
- "multer": "1.4.2",
- "tslib": "2.3.0"
+ "express": "4.17.2",
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"dev": true,
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@@ -18326,19 +17652,19 @@
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+ "resolved": "https://registry.npmjs.org/@nestjs/testing/-/testing-8.2.6.tgz",
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+ "version": "8.0.3",
+ "resolved": "https://registry.npmjs.org/@nestjs/typeorm/-/typeorm-8.0.3.tgz",
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@@ -18474,9 +17800,9 @@
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+ "version": "5.6.3",
+ "resolved": "https://registry.npmjs.org/@octokit/request/-/request-5.6.3.tgz",
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@@ -18484,7 +17810,7 @@
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- "node-fetch": "^2.6.1",
+ "node-fetch": "^2.6.7",
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}
},
@@ -18691,13 +18017,6 @@
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@@ -18707,37 +18026,18 @@
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+ "@semantic-release/error": "^3.0.0",
+ "aggregate-error": "^3.0.0",
+ "debug": "^4.0.0",
+ "dir-glob": "^3.0.0",
+ "escape-string-regexp": "^3.0.0",
+ "form-data": "^4.0.0",
+ "fs-extra": "^10.0.0",
+ "globby": "^11.0.0",
+ "got": "^11.0.0",
+ "lodash": "^4.17.11",
+ "parse-path": "^4.0.0",
+ "url-join": "^4.0.0"
}
},
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@@ -18782,9 +18082,9 @@
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+ "version": "4.4.0",
+ "resolved": "https://registry.npmjs.org/@sindresorhus/is/-/is-4.4.0.tgz",
+ "integrity": "sha512-QppPM/8l3Mawvh4rn9CNEYIU9bxpXUCRMaX9yUpvBk1nMKusLKpfXGDEKExKaPhLzcn3lzil7pR6rnJ11HgeRQ==",
"dev": true
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@@ -18797,9 +18097,9 @@
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+ "version": "8.1.0",
+ "resolved": "https://registry.npmjs.org/@sinonjs/fake-timers/-/fake-timers-8.1.0.tgz",
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"dev": true,
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@@ -18859,9 +18159,9 @@
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+ "version": "7.1.18",
+ "resolved": "https://registry.npmjs.org/@types/babel__core/-/babel__core-7.1.18.tgz",
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@@ -18872,9 +18172,9 @@
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@@ -20088,12 +19350,30 @@
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+ "integrity": "sha1-YuIDvEF2bGwoyfyEMB2rHFMQ+pQ="
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@@ -20180,9 +19460,9 @@
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@@ -23225,9 +22476,9 @@
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+ "resolved": "https://registry.npmjs.org/jest-util/-/jest-util-27.4.2.tgz",
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+ "resolved": "https://registry.npmjs.org/jest-validate/-/jest-validate-27.4.6.tgz",
+ "integrity": "sha512-872mEmCPVlBqbA5dToC57vA3yJaMRfIdpCoD3cyHWJOMx+SJwLNw0I71EkWs41oza/Er9Zno9XuTkRYCPDUJXQ==",
"dev": true,
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"chalk": "^4.0.0",
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+ "version": "6.3.0",
+ "resolved": "https://registry.npmjs.org/camelcase/-/camelcase-6.3.0.tgz",
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@@ -23337,17 +22586,17 @@
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+ "version": "27.4.6",
+ "resolved": "https://registry.npmjs.org/jest-watcher/-/jest-watcher-27.4.6.tgz",
+ "integrity": "sha512-yKQ20OMBiCDigbD0quhQKLkBO+ObGN79MO4nT7YaCuQ5SM+dkBNWE8cZX0FjU6czwMvWw6StWbe+Wv4jJPJ+fw==",
"dev": true,
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- "@jest/types": "^27.1.1",
+ "@jest/test-result": "^27.4.6",
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"chalk": "^4.0.0",
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@@ -23364,9 +22613,9 @@
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+ "version": "27.4.6",
+ "resolved": "https://registry.npmjs.org/jest-worker/-/jest-worker-27.4.6.tgz",
+ "integrity": "sha512-gHWJF/6Xi5CTG5QCvROr6GcmpIqNYpDJyc8A1h/DyXqH1tD6SnRCM0d3U5msV31D2LB/U+E0M+W4oyvKV44oNw==",
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@@ -23437,10 +22686,28 @@
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+ "version": "8.7.0",
+ "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.7.0.tgz",
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"dev": true
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+ "resolved": "https://registry.npmjs.org/form-data/-/form-data-3.0.1.tgz",
+ "integrity": "sha512-RHkBKtLWUVwd7SqRIvCZMEvAMoGUp0XU+seQiZejj0COz3RI3hWP4sCv3gZWWLjJTd7rGwcsF5eKZGii0r/hbg==",
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+ "combined-stream": "^1.0.8",
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+ "ws": {
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+ "resolved": "https://registry.npmjs.org/ws/-/ws-7.5.6.tgz",
+ "integrity": "sha512-6GLgCqo2cy2A2rjCNFlxQS6ZljG/coZfZXclldI8FB/1G3CCI36Zd8xy2HrFVACi8tfk5XrgLQEk+P0Tnz9UcA==",
+ "dev": true,
+ "requires": {}
}
}
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@@ -23536,9 +22803,9 @@
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+ "version": "4.0.5",
+ "resolved": "https://registry.npmjs.org/keyv/-/keyv-4.0.5.tgz",
+ "integrity": "sha512-531pkGLqV3BMg0eDqqJFI0R1mkK1Nm5xIP2mM6keP5P8WfFtCkg2IOwplTUmlGoTgIg9yQYZ/kdihhz89XH3vA==",
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@@ -23574,15 +22841,15 @@
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+ "version": "1.9.46",
+ "resolved": "https://registry.npmjs.org/libphonenumber-js/-/libphonenumber-js-1.9.46.tgz",
+ "integrity": "sha512-QqTX4UVsGy24njtCgLRspiKpxfRniRBZE/P+d0vQXuYWQ+hwDS6X0ouo0O/SRyf7bhhMCE71b6vAvLMtY5PfEw==",
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- "integrity": "sha1-HADHQ7QzzQpOgHWPe2SldEDZ/wA=",
+ "version": "1.2.4",
+ "resolved": "https://registry.npmjs.org/lines-and-columns/-/lines-and-columns-1.2.4.tgz",
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@@ -23645,12 +22912,6 @@
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- "integrity": "sha1-LRd/ZS+jHpObRDjVNBSZ36OCXpk="
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@@ -23689,28 +22940,23 @@
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+ "integrity": "sha1-vMbEmkKihA7Zl/Mj6tpezRguC/4=",
+ "dev": true
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"integrity": "sha1-7dFMgk4sycHgsKG0K7UhBRakJDg="
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+ "version": "1.8.0",
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- "integrity": "sha1-4BpckQnyr3lmDk6LlYd5AYT1qWw=",
+ "version": "1.0.12",
+ "resolved": "https://registry.npmjs.org/makeerror/-/makeerror-1.0.12.tgz",
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@@ -23864,37 +23110,6 @@
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@@ -23904,9 +23119,9 @@
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+ "version": "3.4.1",
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"dev": true,
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@@ -23972,21 +23187,23 @@
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+ "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.3.1.tgz",
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@@ -28995,9 +28075,9 @@
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+ "version": "8.1.1",
+ "resolved": "https://registry.npmjs.org/v8-to-istanbul/-/v8-to-istanbul-8.1.1.tgz",
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@@ -29017,9 +28097,9 @@
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+ "resolved": "https://registry.npmjs.org/validator/-/validator-13.7.0.tgz",
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- "integrity": "sha1-L3+bj9ENZ3JisYqITijRlhjgKPs=",
+ "version": "1.0.8",
+ "resolved": "https://registry.npmjs.org/walker/-/walker-1.0.8.tgz",
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"watchpack": {
- "version": "2.2.0",
- "resolved": "https://registry.npmjs.org/watchpack/-/watchpack-2.2.0.tgz",
- "integrity": "sha512-up4YAn/XHgZHIxFBVCdlMiWDj6WaLKpwVeGQk2I5thdYxF/KmF0aaz6TfJZ/hfl1h/XlcDr7k1KH7ThDagpFaA==",
+ "version": "2.3.1",
+ "resolved": "https://registry.npmjs.org/watchpack/-/watchpack-2.3.1.tgz",
+ "integrity": "sha512-x0t0JuydIo8qCNctdDrn1OzH/qDzk2+rdCOC3YzumZ42fiMqmQ7T3xQurykYMhYfHaPHTp4ZxAx2NfUo1K6QaA==",
"dev": true,
"requires": {
"glob-to-regexp": "^0.4.1",
@@ -29085,9 +28165,9 @@
"dev": true
},
"webpack": {
- "version": "5.52.0",
- "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.52.0.tgz",
- "integrity": "sha512-yRZOat8jWGwBwHpco3uKQhVU7HYaNunZiJ4AkAVQkPCUGoZk/tiIXiwG+8HIy/F+qsiZvSOa+GLQOj3q5RKRYg==",
+ "version": "5.68.0",
+ "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.68.0.tgz",
+ "integrity": "sha512-zUcqaUO0772UuuW2bzaES2Zjlm/y3kRBQDVFVCge+s2Y8mwuUTdperGaAv65/NtRL/1zanpSJOq/MD8u61vo6g==",
"dev": true,
"peer": true,
"requires": {
@@ -29100,12 +28180,12 @@
"acorn-import-assertions": "^1.7.6",
"browserslist": "^4.14.5",
"chrome-trace-event": "^1.0.2",
- "enhanced-resolve": "^5.8.0",
- "es-module-lexer": "^0.7.1",
+ "enhanced-resolve": "^5.8.3",
+ "es-module-lexer": "^0.9.0",
"eslint-scope": "5.1.1",
"events": "^3.2.0",
"glob-to-regexp": "^0.4.1",
- "graceful-fs": "^4.2.4",
+ "graceful-fs": "^4.2.9",
"json-parse-better-errors": "^1.0.2",
"loader-runner": "^4.2.0",
"mime-types": "^2.1.27",
@@ -29113,21 +28193,21 @@
"schema-utils": "^3.1.0",
"tapable": "^2.1.1",
"terser-webpack-plugin": "^5.1.3",
- "watchpack": "^2.2.0",
- "webpack-sources": "^3.2.0"
+ "watchpack": "^2.3.1",
+ "webpack-sources": "^3.2.3"
},
"dependencies": {
"acorn": {
- "version": "8.5.0",
- "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.5.0.tgz",
- "integrity": "sha512-yXbYeFy+jUuYd3/CDcg2NkIYE991XYX/bje7LmjJigUciaeO1JR4XxXgCIV1/Zc/dRuFEyw1L0pbA+qynJkW5Q==",
+ "version": "8.7.0",
+ "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.7.0.tgz",
+ "integrity": "sha512-V/LGr1APy+PXIwKebEWrkZPwoeoF+w1jiOBUmuxuiUIaOHtob8Qc9BTrYo7VuI5fR8tqsy+buA2WFooR5olqvQ==",
"dev": true,
"peer": true
},
"acorn-import-assertions": {
- "version": "1.7.6",
- "resolved": "https://registry.npmjs.org/acorn-import-assertions/-/acorn-import-assertions-1.7.6.tgz",
- "integrity": "sha512-FlVvVFA1TX6l3lp8VjDnYYq7R1nyW6x3svAt4nDgrWQ9SBaSh9CnbwgSUTasgfNfOG5HlM1ehugCvM+hjo56LA==",
+ "version": "1.8.0",
+ "resolved": "https://registry.npmjs.org/acorn-import-assertions/-/acorn-import-assertions-1.8.0.tgz",
+ "integrity": "sha512-m7VZ3jwz4eK6A4Vtt8Ew1/mNbP24u0FhdyfA7fSvnJR6LMdfOYnmuIrrJAgrYfYJ10F/otaHTtrtrtmHdMNzEw==",
"dev": true,
"peer": true,
"requires": {}
@@ -29173,9 +28253,9 @@
}
},
"tapable": {
- "version": "2.2.0",
- "resolved": "https://registry.npmjs.org/tapable/-/tapable-2.2.0.tgz",
- "integrity": "sha512-FBk4IesMV1rBxX2tfiK8RAmogtWn53puLOQlvO8XuwlgxcYbP4mVPS9Ph4aeamSyyVjOl24aYWAuc8U5kCVwMw==",
+ "version": "2.2.1",
+ "resolved": "https://registry.npmjs.org/tapable/-/tapable-2.2.1.tgz",
+ "integrity": "sha512-GNzQvQTOIP6RyTfE2Qxb8ZVlNmw0n88vp1szwWRimP02mnTsx3Wtn5qRdqY9w2XduFNUgvOwhNnQsjwCp+kqaQ==",
"dev": true,
"peer": true
}
@@ -29188,11 +28268,10 @@
"dev": true
},
"webpack-sources": {
- "version": "3.2.0",
- "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.2.0.tgz",
- "integrity": "sha512-fahN08Et7P9trej8xz/Z7eRu8ltyiygEo/hnRi9KqBUs80KeDcnf96ZJo++ewWd84fEf3xSX9bp4ZS9hbw0OBw==",
- "dev": true,
- "peer": true
+ "version": "3.2.3",
+ "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.2.3.tgz",
+ "integrity": "sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w==",
+ "dev": true
},
"whatwg-encoding": {
"version": "1.0.5",
@@ -29293,23 +28372,6 @@
"ansi-styles": "^4.0.0",
"string-width": "^4.1.0",
"strip-ansi": "^6.0.0"
- },
- "dependencies": {
- "is-fullwidth-code-point": {
- "version": "3.0.0",
- "resolved": "https://registry.npmjs.org/is-fullwidth-code-point/-/is-fullwidth-code-point-3.0.0.tgz",
- "integrity": "sha512-zymm5+u+sCsSWyD9qNaejV3DFvhCKclKdizYaJUuHA83RLjb7nSuGnddCHGv0hk+KY7BMAlsWeK4Ueg6EV6XQg=="
- },
- "string-width": {
- "version": "4.2.2",
- "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.2.tgz",
- "integrity": "sha512-XBJbT3N4JhVumXE0eoLU9DCjcaF92KLNqTmFCnG1pf8duUxFGwtP6AD6nkjw9a3IdiRtL3E2w3JDiE/xi3vOeA==",
- "requires": {
- "emoji-regex": "^8.0.0",
- "is-fullwidth-code-point": "^3.0.0",
- "strip-ansi": "^6.0.0"
- }
- }
}
},
"wrappy": {
@@ -29330,9 +28392,9 @@
}
},
"ws": {
- "version": "7.5.5",
- "resolved": "https://registry.npmjs.org/ws/-/ws-7.5.5.tgz",
- "integrity": "sha512-BAkMFcAzl8as1G/hArkxOxq3G7pjUqQ3gzYbLL0/5zNkph70e+lCoxBGnm6AW1+/aiNeV4fnKqZ8m4GZewmH2w==",
+ "version": "8.3.0",
+ "resolved": "https://registry.npmjs.org/ws/-/ws-8.3.0.tgz",
+ "integrity": "sha512-Gs5EZtpqZzLvmIM59w4igITU57lrtYVFneaa434VROv4thzJyV6UjIL3D42lslWlI+D4KzLYnxSwtfuiO79sNw==",
"requires": {}
},
"xml-name-validator": {
@@ -29364,9 +28426,9 @@
"dev": true
},
"xss": {
- "version": "1.0.9",
- "resolved": "https://registry.npmjs.org/xss/-/xss-1.0.9.tgz",
- "integrity": "sha512-2t7FahYnGJys6DpHLhajusId7R0Pm2yTmuL0GV9+mV0ZlaLSnb2toBmppATfg5sWIhZQGlsTLoecSzya+l4EAQ==",
+ "version": "1.0.10",
+ "resolved": "https://registry.npmjs.org/xss/-/xss-1.0.10.tgz",
+ "integrity": "sha512-qmoqrRksmzqSKvgqzN0055UFWY7OKx1/9JWeRswwEVX9fCG5jcYRxa/A2DHcmZX6VJvjzHRQ2STeeVcQkrmLSw==",
"requires": {
"commander": "^2.20.3",
"cssfilter": "0.0.10"
@@ -29400,65 +28462,6 @@
"integrity": "sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg==",
"dev": true
},
- "yargonaut": {
- "version": "1.1.4",
- "resolved": "https://registry.npmjs.org/yargonaut/-/yargonaut-1.1.4.tgz",
- "integrity": "sha512-rHgFmbgXAAzl+1nngqOcwEljqHGG9uUZoPjsdZEs1w5JW9RXYzrSvH/u70C1JE5qFi0qjsdhnUX/dJRpWqitSA==",
- "peer": true,
- "requires": {
- "chalk": "^1.1.1",
- "figlet": "^1.1.1",
- "parent-require": "^1.0.0"
- },
- "dependencies": {
- "ansi-regex": {
- "version": "2.1.1",
- "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-2.1.1.tgz",
- "integrity": "sha1-w7M6te42DYbg5ijwRorn7yfWVN8=",
- "peer": true
- },
- "ansi-styles": {
- "version": "2.2.1",
- "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-2.2.1.tgz",
- "integrity": "sha1-tDLdM1i2NM914eRmQ2gkBTPB3b4=",
- "peer": true
- },
- "chalk": {
- "version": "1.1.3",
- "resolved": "https://registry.npmjs.org/chalk/-/chalk-1.1.3.tgz",
- "integrity": "sha1-qBFcVeSnAv5NFQq9OHKCKn4J/Jg=",
- "peer": true,
- "requires": {
- "ansi-styles": "^2.2.1",
- "escape-string-regexp": "^1.0.2",
- "has-ansi": "^2.0.0",
- "strip-ansi": "^3.0.0",
- "supports-color": "^2.0.0"
- }
- },
- "escape-string-regexp": {
- "version": "1.0.5",
- "resolved": "https://registry.npmjs.org/escape-string-regexp/-/escape-string-regexp-1.0.5.tgz",
- "integrity": "sha1-G2HAViGQqN/2rjuyzwIAyhMLhtQ=",
- "peer": true
- },
- "strip-ansi": {
- "version": "3.0.1",
- "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
- "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
- "peer": true,
- "requires": {
- "ansi-regex": "^2.0.0"
- }
- },
- "supports-color": {
- "version": "2.0.0",
- "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-2.0.0.tgz",
- "integrity": "sha1-U10EXOa2Nj+kARcIRimZXp3zJMc=",
- "peer": true
- }
- }
- },
"yargs": {
"version": "16.2.0",
"resolved": "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz",
@@ -29471,23 +28474,6 @@
"string-width": "^4.2.0",
"y18n": "^5.0.5",
"yargs-parser": "^20.2.2"
- },
- "dependencies": {
- "is-fullwidth-code-point": {
- "version": "3.0.0",
- "resolved": "https://registry.npmjs.org/is-fullwidth-code-point/-/is-fullwidth-code-point-3.0.0.tgz",
- "integrity": "sha512-zymm5+u+sCsSWyD9qNaejV3DFvhCKclKdizYaJUuHA83RLjb7nSuGnddCHGv0hk+KY7BMAlsWeK4Ueg6EV6XQg=="
- },
- "string-width": {
- "version": "4.2.2",
- "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.2.tgz",
- "integrity": "sha512-XBJbT3N4JhVumXE0eoLU9DCjcaF92KLNqTmFCnG1pf8duUxFGwtP6AD6nkjw9a3IdiRtL3E2w3JDiE/xi3vOeA==",
- "requires": {
- "emoji-regex": "^8.0.0",
- "is-fullwidth-code-point": "^3.0.0",
- "strip-ansi": "^6.0.0"
- }
- }
}
},
"yargs-parser": {
@@ -29501,12 +28487,6 @@
"integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==",
"dev": true
},
- "yocto-queue": {
- "version": "0.1.0",
- "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
- "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==",
- "dev": true
- },
"zen-observable": {
"version": "0.8.15",
"resolved": "https://registry.npmjs.org/zen-observable/-/zen-observable-0.8.15.tgz",
diff --git a/api/package.json b/api/package.json
index 62199f765340b2e6aa14e57a16751b9b49474f29..dcf94cb22d1f2fac01d0fc75470de28a9dae068d 100644
--- a/api/package.json
+++ b/api/package.json
@@ -18,7 +18,8 @@
"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",
+ "test:we2e": "jest --watch --config ./test/jest.e2e-config.ts",
"prepare": "cd .. && husky install api/.husky"
},
"dependencies": {
@@ -42,7 +43,7 @@
"@eclass/semantic-release-docker": "^2.0.0",
"@nestjs/cli": "^8.0.0",
"@nestjs/schematics": "^8.0.0",
- "@nestjs/testing": "^8.0.0",
+ "@nestjs/testing": "^8.2.2",
"@semantic-release/changelog": "^6.0.1",
"@semantic-release/git": "^10.0.1",
"@semantic-release/gitlab": "^7.0.4",
@@ -83,6 +84,7 @@
"testEnvironment": "node"
},
"release": {
+ "tagFormat": "${version}",
"plugins": [
"@semantic-release/commit-analyzer",
"@semantic-release/release-notes-generator",
diff --git a/api/src/common/interfaces/utilities.interface.ts b/api/src/common/interfaces/utilities.interface.ts
index ddf5dedfa9585bdffa46ef5a90ca643d49eacf7a..efcb1cd621628c288d0f7d6d5b674275add8d4b8 100644
--- a/api/src/common/interfaces/utilities.interface.ts
+++ b/api/src/common/interfaces/utilities.interface.ts
@@ -1 +1,14 @@
export type Dictionary<T> = { [key: string]: T };
+
+export enum MIME_TYPES {
+ ERROR = 'text/plain+error',
+ WARNING = 'text/plain+warning',
+ USER_WARNING = 'text/plain+user_error',
+ HIGHCHARTS = 'application/vnd.highcharts+json',
+ JSON = 'application/json',
+ JSONBTREE = 'application/binary-tree+json',
+ PFA = 'application/pfa+json',
+ JSONDATA = 'application/vnd.dataresource+json',
+ HTML = 'text/html',
+ TEXT = 'text/plain',
+}
diff --git a/api/src/engine/connectors/csv/main.connector.ts b/api/src/engine/connectors/csv/main.connector.ts
index 05864adb55c7141de3ec49bd6854b5fdcdb793ee..c9c2b6fd71a69082dbfc95d670c0a8d7a9d4ee87 100644
--- a/api/src/engine/connectors/csv/main.connector.ts
+++ b/api/src/engine/connectors/csv/main.connector.ts
@@ -41,18 +41,16 @@ export default class CSVService implements IEngineService {
throw new Error('Method not implemented.');
}
- getExperiment(uuid: string): Experiment | Promise<Experiment> {
+ getExperiment(id: string): Experiment | Promise<Experiment> {
throw new Error('Method not implemented.');
}
- removeExperiment(
- uuid: string,
- ): PartialExperiment | Promise<PartialExperiment> {
+ removeExperiment(id: string): PartialExperiment | Promise<PartialExperiment> {
throw new Error('Method not implemented.');
}
editExperient(
- uuid: string,
+ id: string,
expriment: ExperimentEditInput,
): Experiment | Promise<Experiment> {
throw new Error('Method not implemented.');
diff --git a/api/src/engine/connectors/datashield/main.connector.ts b/api/src/engine/connectors/datashield/main.connector.ts
index 4df8aa14bf1fda0bdec3a4d21c98cc79277cdd83..0b884a9061ef1ad789cb6886f4d125670476337b 100644
--- a/api/src/engine/connectors/datashield/main.connector.ts
+++ b/api/src/engine/connectors/datashield/main.connector.ts
@@ -1,5 +1,5 @@
-import { Observable } from 'rxjs';
-import { IEngineService } from 'src/engine/engine.interfaces';
+import { firstValueFrom, Observable } from 'rxjs';
+import { IEngineOptions, IEngineService } from 'src/engine/engine.interfaces';
import { Domain } from 'src/engine/models/domain.model';
import { ExperimentCreateInput } from 'src/engine/models/experiment/input/experiment-create.input';
import {
@@ -9,8 +9,20 @@ import {
import { ListExperiments } from 'src/engine/models/experiment/list-experiments.model';
import { ExperimentEditInput } from 'src/engine/models/experiment/input/experiment-edit.input';
import { Algorithm } from 'src/engine/models/experiment/algorithm.model';
+import { ENGINE_MODULE_OPTIONS } from 'src/engine/engine.constants';
+import { Inject } from '@nestjs/common';
+import { HttpService } from '@nestjs/axios';
+import { REQUEST } from '@nestjs/core';
+import { Request } from 'express';
+import { transformToDomains } from './transformations';
export default class DataShieldService implements IEngineService {
+ constructor(
+ @Inject(ENGINE_MODULE_OPTIONS) private readonly options: IEngineOptions,
+ private readonly httpService: HttpService,
+ @Inject(REQUEST) private readonly req: Request,
+ ) {}
+
logout(): void {
throw new Error('Method not implemented.');
}
@@ -33,29 +45,41 @@ export default class DataShieldService implements IEngineService {
throw new Error('Method not implemented.');
}
- getExperiment(uuid: string): Experiment | Promise<Experiment> {
+ getExperiment(id: string): Experiment | Promise<Experiment> {
throw new Error('Method not implemented.');
}
- removeExperiment(
- uuid: string,
- ): PartialExperiment | Promise<PartialExperiment> {
+ removeExperiment(id: string): PartialExperiment | Promise<PartialExperiment> {
throw new Error('Method not implemented.');
}
editExperient(
- uuid: string,
+ id: string,
expriment: ExperimentEditInput,
): Experiment | Promise<Experiment> {
throw new Error('Method not implemented.');
}
- getDomains(): Domain[] {
- throw new Error('Method not implemented.');
+ async getDomains(): Promise<Domain[]> {
+ const path = this.options.baseurl + 'start';
+
+ const data = await firstValueFrom(
+ this.httpService.get(path, {
+ auth: { username: 'guest', password: 'guest123' },
+ }),
+ );
+ return [transformToDomains.evaluate(data.data)];
}
getActiveUser(): string {
- throw new Error('Method not implemented.');
+ const dummyUser = {
+ username: 'anonymous',
+ subjectId: 'anonymousId',
+ fullname: 'anonymous',
+ email: 'anonymous@anonymous.com',
+ agreeNDA: true,
+ };
+ return JSON.stringify(dummyUser);
}
editActiveUser(): Observable<string> {
@@ -83,10 +107,10 @@ export default class DataShieldService implements IEngineService {
}
getExperiments(): string {
- throw new Error('Method not implemented.');
+ return '[]';
}
getAlgorithmsREST(): string {
- throw new Error('Method not implemented.');
+ return '[]';
}
}
diff --git a/api/src/engine/connectors/datashield/transformations.ts b/api/src/engine/connectors/datashield/transformations.ts
new file mode 100644
index 0000000000000000000000000000000000000000..77302eb169ec09ceca138657252d428364dde62c
--- /dev/null
+++ b/api/src/engine/connectors/datashield/transformations.ts
@@ -0,0 +1,28 @@
+// This file contains all transformation queries for JSONata
+// see : https://docs.jsonata.org/
+
+import * as jsonata from 'jsonata';
+
+export const transformToDomains = jsonata(`
+{
+ "id": "sophia",
+ "datasets": datasets.{
+ "id": $.id[0],
+ "label": $.label[0]
+ },
+ "rootGroup": {
+ "id": "rootGroup",
+ "label": "Root group",
+ "groups": groups.id
+ },
+ "groups": groups.{
+ "id": $.id[0],
+ "label": $.label[0],
+ "variables": $.variables
+ },
+ "variables": $distinct(groups.variables).{
+ "id": $,
+ "label": $
+ }
+}
+`);
diff --git a/api/src/engine/connectors/exareme/converters.ts b/api/src/engine/connectors/exareme/converters.ts
index e9bc1d7c51908d9b833500d70e573774b908a221..5ca4b79db61a06924af99aebb4e0ca44670de630 100644
--- a/api/src/engine/connectors/exareme/converters.ts
+++ b/api/src/engine/connectors/exareme/converters.ts
@@ -1,7 +1,9 @@
+import { MIME_TYPES } from 'src/common/interfaces/utilities.interface';
import { Category } from 'src/engine/models/category.model';
-import { AlgorithmParameter } from 'src/engine/models/experiment/algorithm-parameter.model';
+import { Dataset } from 'src/engine/models/dataset.model';
import { Algorithm } from 'src/engine/models/experiment/algorithm.model';
import { Experiment } from 'src/engine/models/experiment/experiment.model';
+import { AlgorithmParamInput } from 'src/engine/models/experiment/input/algorithm-parameter.input';
import { ExperimentCreateInput } from 'src/engine/models/experiment/input/experiment-create.input';
import { Group } from 'src/engine/models/group.model';
import { ResultUnion } from 'src/engine/models/result/common/result-union.model';
@@ -9,14 +11,19 @@ import {
GroupResult,
GroupsResult,
} from 'src/engine/models/result/groups-result.model';
+import { HeatMapResult } from 'src/engine/models/result/heat-map-result.model';
+import { LineChartResult } from 'src/engine/models/result/line-chart-result.model';
import { RawResult } from 'src/engine/models/result/raw-result.model';
import { Variable } from 'src/engine/models/variable.model';
import { Entity } from './interfaces/entity.interface';
import { ExperimentData } from './interfaces/experiment/experiment.interface';
+import { ResultChartExperiment } from './interfaces/experiment/result-chart-experiment.interface';
import { ResultExperiment } from './interfaces/experiment/result-experiment.interface';
import { Hierarchy } from './interfaces/hierarchy.interface';
import { VariableEntity } from './interfaces/variable-entity.interface';
import {
+ dataROCToLineResult,
+ dataToHeatmap,
descriptiveModelToTables,
descriptiveSingleToTables,
transformToAlgorithms,
@@ -43,6 +50,14 @@ export const dataToCategory = (data: Entity): Category => {
};
};
+export const dataToDataset = (data: Entity): Dataset => {
+ return {
+ id: data.code,
+ label: data.label,
+ isLongitudinal: !!data.code.toLowerCase().includes('longitudinal'),
+ };
+};
+
export const dataToVariable = (data: VariableEntity): Variable => {
return {
id: data.code,
@@ -56,11 +71,11 @@ export const dataToVariable = (data: VariableEntity): Variable => {
};
};
-const algoParamInputToData = (param: AlgorithmParameter) => {
+const algoParamInputToData = (param: AlgorithmParamInput) => {
return {
- name: param.name,
- label: param.name,
- value: param.value.join(','),
+ name: param.id,
+ label: param.id,
+ value: param.value,
};
};
@@ -69,7 +84,7 @@ export const experimentInputToData = (data: ExperimentCreateInput) => {
((data.transformations?.length > 0 || data.interactions?.length > 0) && {
single:
data.transformations?.map((t) => ({
- var_name: t.name,
+ var_name: t.id,
unary_operation: t.operation,
})) || [],
interactions:
@@ -79,7 +94,7 @@ export const experimentInputToData = (data: ExperimentCreateInput) => {
}) ||
null;
- return {
+ const params = {
algorithm: {
parameters: [
{
@@ -97,11 +112,6 @@ export const experimentInputToData = (data: ExperimentCreateInput) => {
label: 'pathology',
value: data.domain,
},
- {
- name: 'y',
- label: 'y',
- value: data.variables.join(','),
- },
...(formula
? [
{
@@ -112,10 +122,59 @@ export const experimentInputToData = (data: ExperimentCreateInput) => {
: []),
].concat(data.algorithm.parameters.map(algoParamInputToData)),
type: data.algorithm.type ?? 'string',
- name: data.algorithm.name,
+ name: data.algorithm.id,
},
name: data.name,
};
+
+ if (data.coVariables && data.coVariables.length) {
+ let separator = ',';
+
+ const design = params.algorithm.parameters.find((p) => p.name === 'design');
+ const excludes = [
+ 'Multiple Histograms',
+ 'CART',
+ 'ID3',
+ 'Naive Bayes Training',
+ ];
+
+ if (design && !excludes.includes(data.algorithm.id)) {
+ separator = design.value === 'additive' ? '+' : '*';
+ }
+
+ params.algorithm.parameters.push({
+ name: 'x',
+ label: 'x',
+ value: data.coVariables.join(separator),
+ });
+ }
+
+ if (data.variables) {
+ let variables = data.variables.join(',');
+
+ if (data.algorithm.id === 'TTEST_PAIRED') {
+ const varCount = data.variables.length;
+ variables = data.variables
+ ?.reduce(
+ (vectors: string, v, i) =>
+ (i + 1) % 2 === 0
+ ? `${vectors}${v},`
+ : varCount === i + 1
+ ? `${vectors}${v}-${data.variables[0]}`
+ : `${vectors}${v}-`,
+ '',
+ )
+ .replace(/,$/, '');
+ }
+
+ params.algorithm.parameters.push({
+ name: 'y',
+ label: 'y',
+ value: variables,
+ });
+ }
+
+ return params;
};
export const descriptiveDataToTableResult = (
@@ -143,31 +202,56 @@ export const descriptiveDataToTableResult = (
return [result];
};
-export const dataToExperiment = (data: ExperimentData): Experiment => {
- const expTransform = transformToExperiment.evaluate(data);
+export const dataToExperiment = (
+ data: ExperimentData,
+): Experiment | undefined => {
+ try {
+ const expTransform = transformToExperiment.evaluate(data);
- const exp: Experiment = {
- ...expTransform,
- results: [],
- };
+ const exp: Experiment = {
+ ...expTransform,
+ results: [],
+ };
- exp.results = data.result
- ? data.result
- .map((result) => dataToResult(result, exp.algorithm.name))
- .flat()
- : [];
+ exp.results = data.result
+ ? data.result
+ .map((result) => dataToResult(result, exp.algorithm.id))
+ .flat()
+ : [];
- return exp;
+ return exp;
+ } catch (e) {
+ return {
+ id: data.uuid,
+ name: data.name,
+ status: 'error',
+ variables: [],
+ domain: data['domain'] ?? '',
+ datasets: [],
+ algorithm: {
+ id: 'unknown',
+ },
+ };
+ }
};
export const dataToAlgorithms = (data: string): Algorithm[] => {
return transformToAlgorithms.evaluate(data);
};
-export const dataToRaw = (result: ResultExperiment): RawResult[] => {
+export const dataToRaw = (
+ algo: string,
+ result: ResultExperiment,
+): RawResult[] => {
+ let data = result;
+
+ if (algo === 'CART') {
+ data = { ...data, type: MIME_TYPES.JSONBTREE };
+ }
+
return [
{
- rawdata: result.data,
+ rawdata: data,
},
];
};
@@ -179,8 +263,10 @@ export const dataToResult = (
switch (result.type.toLowerCase()) {
case 'application/json':
return dataJSONtoResult(result, algo);
+ case 'application/vnd.highcharts+json':
+ return dataHighchartToResult(result as ResultChartExperiment, algo);
default:
- return dataToRaw(result);
+ return dataToRaw(algo, result);
}
};
@@ -192,6 +278,20 @@ export const dataJSONtoResult = (
case 'descriptive_stats':
return descriptiveDataToTableResult(result);
default:
- return [];
+ return dataToRaw(algo, result);
+ }
+};
+
+export const dataHighchartToResult = (
+ result: ResultChartExperiment,
+ algo: string,
+): Array<typeof ResultUnion> => {
+ switch (result.data.chart.type) {
+ case 'heatmap':
+ return [dataToHeatmap.evaluate(result) as HeatMapResult];
+ case 'area':
+ return [dataROCToLineResult.evaluate(result) as LineChartResult];
+ default:
+ return dataToRaw(algo, result);
}
};
diff --git a/api/src/engine/connectors/exareme/interfaces/experiment/experiment.interface.ts b/api/src/engine/connectors/exareme/interfaces/experiment/experiment.interface.ts
index 7412cb0560c9eda88fe61dd4ebbf8128c94e2c62..cd5ceb45a4539812ec15cb94755f2302bb99de63 100644
--- a/api/src/engine/connectors/exareme/interfaces/experiment/experiment.interface.ts
+++ b/api/src/engine/connectors/exareme/interfaces/experiment/experiment.interface.ts
@@ -5,6 +5,7 @@ export interface ExperimentData {
uuid?: string;
status?: string;
createdBy?: string;
+ created: string;
shared?: boolean;
viewed?: boolean;
result?: ResultExperiment[];
diff --git a/api/src/engine/connectors/exareme/interfaces/experiment/result-chart-experiment.interface.ts b/api/src/engine/connectors/exareme/interfaces/experiment/result-chart-experiment.interface.ts
new file mode 100644
index 0000000000000000000000000000000000000000..ef0ba339600d418e2ed02a484dfebcfc5ab8b32b
--- /dev/null
+++ b/api/src/engine/connectors/exareme/interfaces/experiment/result-chart-experiment.interface.ts
@@ -0,0 +1,9 @@
+export interface ResultChartExperiment {
+ data: {
+ chart: {
+ type: string;
+ };
+ series: unknown;
+ };
+ type: string;
+}
diff --git a/api/src/engine/connectors/exareme/interfaces/test-utilities.ts b/api/src/engine/connectors/exareme/interfaces/test-utilities.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2ad1c79e8384dfb1a12fe8dbe75511720dfe4e1f
--- /dev/null
+++ b/api/src/engine/connectors/exareme/interfaces/test-utilities.ts
@@ -0,0 +1,81 @@
+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 ${TIMEOUT_DURATION_SECONDS} s`,
+ );
+ }
+
+ elapsed = elapsed + 0.3;
+ }, 300);
+ });
+
+const uid = (): string =>
+ 'xxxxxxxx'.replace(/[xy]/g, (c) => {
+ const r = (Math.random() * 16) | 0;
+ const v = c === 'x' ? r : (r & 0x3) | 0x8;
+
+ return v.toString(16);
+ });
+
+const generateNumber = (): string => {
+ return Math.round(Math.random() * 10000).toString();
+};
+export {
+ createExperiment,
+ uid,
+ waitForResult,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+};
diff --git a/api/src/engine/connectors/exareme/main.connector.ts b/api/src/engine/connectors/exareme/main.connector.ts
index 146fb4308b44b7a189b1f31cadcd37e0c35cd8c0..5733366f9125337a555ff7f7df7faad52dae6627 100644
--- a/api/src/engine/connectors/exareme/main.connector.ts
+++ b/api/src/engine/connectors/exareme/main.connector.ts
@@ -24,7 +24,7 @@ import { Group } from 'src/engine/models/group.model';
import { Variable } from 'src/engine/models/variable.model';
import {
dataToAlgorithms,
- dataToCategory,
+ dataToDataset,
dataToExperiment,
dataToGroup,
dataToVariable,
@@ -74,7 +74,7 @@ export default class ExaremeService implements IEngineService {
return {
...resultAPI.data,
- experiments: resultAPI.data.experiments.map(dataToExperiment),
+ experiments: resultAPI.data.experiments?.map(dataToExperiment) ?? [],
};
}
@@ -86,8 +86,8 @@ export default class ExaremeService implements IEngineService {
return dataToAlgorithms(resultAPI.data);
}
- async getExperiment(uuid: string): Promise<Experiment> {
- const path = this.options.baseurl + `experiments/${uuid}`;
+ async getExperiment(id: string): Promise<Experiment> {
+ const path = this.options.baseurl + `experiments/${id}`;
const resultAPI = await firstValueFrom(
this.httpService.get<ExperimentData>(path),
@@ -97,10 +97,10 @@ export default class ExaremeService implements IEngineService {
}
async editExperient(
- uuid: string,
+ id: string,
expriment: ExperimentEditInput,
): Promise<Experiment> {
- const path = this.options.baseurl + `experiments/${uuid}`;
+ const path = this.options.baseurl + `experiments/${id}`;
const resultAPI = await firstValueFrom(
this.httpService.patch<ExperimentData>(path, expriment),
@@ -109,16 +109,16 @@ export default class ExaremeService implements IEngineService {
return dataToExperiment(resultAPI.data);
}
- async removeExperiment(uuid: string): Promise<PartialExperiment> {
- const path = this.options.baseurl + `experiments/${uuid}`;
+ async removeExperiment(id: string): Promise<PartialExperiment> {
+ const path = this.options.baseurl + `experiments/${id}`;
try {
await firstValueFrom(this.httpService.delete(path));
return {
- uuid: uuid,
+ id: id,
};
} catch (error) {
- throw new BadRequestException(`${uuid} does not exists`);
+ throw new BadRequestException(`${id} does not exists`);
}
}
@@ -141,7 +141,7 @@ export default class ExaremeService implements IEngineService {
label: data.label,
groups: groups,
rootGroup: dataToGroup(data.metadataHierarchy),
- datasets: data.datasets ? data.datasets.map(dataToCategory) : [],
+ datasets: data.datasets ? data.datasets.map(dataToDataset) : [],
variables: data.metadataHierarchy
? this.flattenVariables(data.metadataHierarchy, groups)
: [],
@@ -172,22 +172,22 @@ export default class ExaremeService implements IEngineService {
.pipe(map((response) => response.data));
}
- getExperimentREST(uuid: string): Observable<string> {
- const path = this.options.baseurl + `experiments/${uuid}`;
+ getExperimentREST(id: string): Observable<string> {
+ const path = this.options.baseurl + `experiments/${id}`;
return this.httpService
.get<string>(path)
.pipe(map((response) => response.data));
}
- deleteExperiment(uuid: string): Observable<string> {
- const path = this.options.baseurl + `experiments/${uuid}`;
+ deleteExperiment(id: string): Observable<string> {
+ const path = this.options.baseurl + `experiments/${id}`;
return this.httpService.delete(path).pipe(map((response) => response.data));
}
- editExperimentREST(uuid: string): Observable<string> {
- const path = this.options.baseurl + `experiments/${uuid}`;
+ editExperimentREST(id: string): Observable<string> {
+ const path = this.options.baseurl + `experiments/${id}`;
return this.httpService
.patch(path, this.req.body)
diff --git a/api/src/engine/connectors/exareme/tests/e2e/3c.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/3c.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..8770e901a69a2cfbb5575f079e2d7c65bcd32b0f
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/3c.e2e-spec.ts
@@ -0,0 +1,74 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+
+ const modelSlug = `3c-${generateNumber()}`;
+ const algorithmId = 'THREE_C';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['lefthippocampus', 'righthippocampus', 'leftcaudate'],
+ coVariables: ['gender', 'agegroup'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code === 'ppmi' || d.code === 'edsd')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ { id: 'dx', value: 'alzheimerbroadcategory' },
+ { id: 'c2_feature_selection_method', value: 'RF' },
+ { id: 'c2_num_clusters_method', value: 'Euclidean' },
+ { id: 'c2_num_clusters', value: '6' },
+ { id: 'c2_clustering_method', value: 'Euclidean' },
+ { id: 'c3_feature_selection_method', value: 'RF' },
+ { id: 'c3_classification_method', value: 'RF' },
+ ],
+ },
+ filter: '',
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(1);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/calibration-belt.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/calibration-belt.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..447b8f457dafe655ee12d7d518bcf8b0fc7d37c7
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/calibration-belt.e2e-spec.ts
@@ -0,0 +1,87 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+
+ const modelSlug = `calibration-belt-${generateNumber()}`;
+ 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 ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult.status).toStrictEqual('success');
+ expect(experimentResult).toBeTruthy();
+
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(1);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/cart.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/cart.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..f8b0085449c7a0229044d66cd73b09a727149ce1
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/cart.e2e-spec.ts
@@ -0,0 +1,72 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { RawResult } from 'src/engine/models/result/raw-result.model';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `cart-${generateNumber()}`;
+ const algorithmId = 'CART';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ coVariables: ['lefthippocampus', 'righthippocampus'],
+ variables: ['alzheimerbroadcategory'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ { id: 'max_depth', value: '3' },
+ { id: 'no_split_points', value: '10' },
+ ],
+ },
+ 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).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(1);
+ const r0 = experimentResult.results[0] as RawResult;
+
+ expect(r0?.rawdata['data'].gain).toEqual(0.6142216049382716);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/descriptiveStatistics.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/descriptiveStatistics.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..5808b159dae93067640e66ade63f82a15ab3debb
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/descriptiveStatistics.e2e-spec.ts
@@ -0,0 +1,76 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { GroupsResult } from 'src/engine/models/result/groups-result.model';
+import { TableResult } from 'src/engine/models/result/table-result.model';
+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,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/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 = `statistics-${generateNumber()}`;
+ const algorithmId = 'DESCRIPTIVE_STATS';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['lefthippocampus', 'alzheimerbroadcategory'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [],
+ },
+ filter: '',
+ transformations: [
+ {
+ id: 'lefthippocampus',
+ operation: 'standardize',
+ },
+ ],
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(1);
+ const r0 = experimentResult.results[0] as GroupsResult;
+ const table = r0.groups[0].results[0] as TableResult;
+
+ expect(table.data[0][2]).toEqual(474);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/id3.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/id3.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..4ef963a6ca5ab93cbe07bf0ff422e40a94744413
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/id3.e2e-spec.ts
@@ -0,0 +1,69 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { RawResult } from 'src/engine/models/result/raw-result.model';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `id3-${generateNumber()}`;
+ const algorithmId = 'ID3';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['alzheimerbroadcategory'],
+ coVariables: ['gender', 'agegroup'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [{ id: 'iterations_max_number', value: '20' }],
+ },
+ filter: '',
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(2);
+ const data = experimentResult.results[0] as RawResult;
+
+ expect(data.rawdata['data']['data'][0][2]).toEqual('+80y');
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/k-means.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/k-means.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..57054721ff0675b01d5865ca312bcaa5335e143f
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/k-means.e2e-spec.ts
@@ -0,0 +1,84 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { RawResult } from 'src/engine/models/result/raw-result.model';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `kmeans-${generateNumber()}`;
+ const algorithmId = 'KMEANS';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['leftacgganteriorcingulategyrus', 'rightcerebellumexterior'],
+ coVariables: ['alzheimerbroadcategory'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ {
+ id: 'k',
+ value: '4',
+ },
+ {
+ id: 'e',
+ value: '1',
+ },
+ {
+ id: 'iterations_max_number',
+ value: '1000',
+ },
+ ],
+ },
+ filter: '',
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(1);
+ const data = experimentResult.results[0] as RawResult;
+
+ expect(
+ data.rawdata['data'][2]['leftacgganteriorcingulategyrus'],
+ ).toBeCloseTo(4.197, 2);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/kaplan-meier.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/kaplan-meier.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..b0766164343410b79c98588100c3a43d037b4df1
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/kaplan-meier.e2e-spec.ts
@@ -0,0 +1,82 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `kaplan-meier-${generateNumber()}`;
+ const algorithmId = 'KAPLAN_MEIER';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['alzheimerbroadcategory'],
+ coVariables: ['apoe4'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ {
+ id: 'outcome_pos',
+ value: 'AD',
+ },
+ {
+ id: 'outcome_neg',
+ value: 'MCI',
+ },
+ {
+ id: 'max_age',
+ value: '100',
+ },
+ {
+ id: 'total_duration',
+ value: '1100',
+ },
+ ],
+ },
+ filter: '',
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(1);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/linear-regression.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/linear-regression.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..4ed7f222182726313aaaafde67af362e4f748cc1
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/linear-regression.e2e-spec.ts
@@ -0,0 +1,91 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { RawResult } from 'src/engine/models/result/raw-result.model';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `linear-${generateNumber()}`;
+ const algorithmId = 'LINEAR_REGRESSION';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['lefthippocampus'],
+ coVariables: ['leftpcuprecuneus'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ {
+ id: 'referencevalues',
+ value: '[{"name":"alzheimerbroadcategory","val":"Other"}]',
+ },
+ {
+ id: 'encodingparameter',
+ value: 'dummycoding',
+ },
+ {
+ id: 'filter',
+ value:
+ '{"condition":"AND","rules":[{"id":"subjectageyears","field":"subjectageyears","type":"integer","input":"number","operator":"greater","value":"65"}],"valid":true}',
+ },
+ ],
+ },
+ filter:
+ '{"condition":"AND","rules":[{"id":"subjectageyears","field":"subjectageyears","type":"integer","input":"number","operator":"greater","value":"65"}],"valid":true}',
+ };
+
+ 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).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(1);
+ const data = experimentResult.results[0] as RawResult;
+
+ expect(data.rawdata['data']['coefficients'][0]['estimate']).toBeCloseTo(
+ 0.986,
+ 3,
+ );
+ expect(data.rawdata['data']['statistics'][0]['value']).toBeCloseTo(
+ -1.478,
+ 3,
+ );
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/logistic-regression.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/logistic-regression.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..abc045cd32efb98cd61908c77bd5a122719d7a41
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/logistic-regression.e2e-spec.ts
@@ -0,0 +1,72 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { RawResult } from 'src/engine/models/result/raw-result.model';
+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,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/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 = `logistic-${generateNumber()}`;
+ const algorithmId = 'LOGISTIC_REGRESSION';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['gender'],
+ coVariables: ['lefthippocampus'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ { id: 'positive_level', value: 'M' },
+ { id: 'negative_level', value: 'F' },
+ ],
+ },
+ filter: '',
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(1);
+ const data = experimentResult.results[0] as RawResult;
+
+ expect(data.rawdata['data']['Coefficients'][0]).toBeCloseTo(-7.628, 3);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/multiple-histograms.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/multiple-histograms.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7604dd93bd27b021f0437fd5c87304135b80957d
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/multiple-histograms.e2e-spec.ts
@@ -0,0 +1,65 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `histograms-${generateNumber()}`;
+ const algorithmId = 'MULTIPLE_HISTOGRAMS';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['lefthippocampus'],
+ coVariables: ['gender', 'alzheimerbroadcategory'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [{ id: 'bins', value: '{ "lefthippocampus" : 35 }' }],
+ },
+ filter: '',
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(3);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/naive-bayes.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/naive-bayes.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..024e41227e8642e6896882d09213b02b7510ec25
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/naive-bayes.e2e-spec.ts
@@ -0,0 +1,78 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import { RawResult } from '../../../../models/result/raw-result.model';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `naivebayes-${generateNumber()}`;
+ const algorithmId = 'NAIVE_BAYES';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['alzheimerbroadcategory'],
+ coVariables: ['righthippocampus', 'lefthippocampus'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ {
+ id: 'alpha',
+ value: '0.1',
+ },
+ {
+ id: 'k',
+ value: '10',
+ },
+ ],
+ },
+ filter: '',
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(5);
+ const data = experimentResult.results[0] as RawResult;
+
+ expect(data.rawdata['data']['precision'][0]).toBeCloseTo(0.517, 3);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/one-way-anova.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/one-way-anova.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e8361797cd5805a1f84e4e8601d110e8ef344a9e
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/one-way-anova.e2e-spec.ts
@@ -0,0 +1,65 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import { RawResult } from '../../../../models/result/raw-result.model';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `anova-1way-${generateNumber()}`;
+ const algorithmId = 'ANOVA_ONEWAY';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['lefthippocampus'],
+ coVariables: ['ppmicategory'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code === 'ppmi')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [],
+ },
+ filter: '',
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(4);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/pca.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/pca.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..79f65b81638c405455cdcf2288ce4fd46a6b3a59
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/pca.e2e-spec.ts
@@ -0,0 +1,71 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import { RawResult } from '../../../../models/result/raw-result.model';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `pca-${generateNumber()}`;
+ const algorithmId = 'PCA';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['lefthippocampus', 'rightthalamusproper', 'leftthalamusproper'],
+ coVariables: ['alzheimerbroadcategory'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ { id: 'standardize', value: 'false' },
+ { id: 'coding', value: 'null' },
+ ],
+ },
+ filter: '',
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(4);
+ const data = experimentResult.results[0] as RawResult;
+
+ expect(data.rawdata['data']['eigenvalues'][1]).toBeCloseTo(0.433, 3);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/pearson-correlation.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/pearson-correlation.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e1617dd43649650676c7eb41f7c3227158a1bec2
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/pearson-correlation.e2e-spec.ts
@@ -0,0 +1,73 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import { RawResult } from '../../../../models/result/raw-result.model';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `pearson-${generateNumber()}`;
+ const algorithmId = 'PEARSON_CORRELATION';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['righthippocampus'],
+ coVariables: ['lefthippocampus'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ { id: 'standardize', value: 'false' },
+ { id: 'coding', value: 'null' },
+ ],
+ },
+ 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).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(2);
+ const data = experimentResult.results[0] as RawResult;
+
+ expect(
+ data.rawdata['data']['Pearson correlation coefficient'][0][0],
+ ).toBeCloseTo(0.924, 3);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/t-test-independant.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/t-test-independant.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2dee1858887a161e31f114f0343660847b676215
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/t-test-independant.e2e-spec.ts
@@ -0,0 +1,101 @@
+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 { RawResult } from '../../../../models/result/raw-result.model';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/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 = `ttest-idp-${generateNumber()}`;
+ const algorithmId = 'TTEST_INDEPENDENT';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: [
+ 'rightpcggposteriorcingulategyrus',
+ 'leftpcggposteriorcingulategyrus',
+ 'rightacgganteriorcingulategyrus',
+ 'leftacgganteriorcingulategyrus',
+ 'rightmcggmiddlecingulategyrus',
+ 'leftmcggmiddlecingulategyrus',
+ 'rightphgparahippocampalgyrus',
+ ],
+ coVariables: ['gender'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ {
+ id: 'xlevels',
+ value: 'M,F',
+ },
+ {
+ id: 'testvalue',
+ value: '3.0',
+ },
+ {
+ id: 'hypothesis',
+ value: 'greaterthan',
+ },
+ {
+ id: 'effectsize',
+ value: '1',
+ },
+ {
+ id: 'ci',
+ value: '1',
+ },
+ {
+ id: 'meandiff',
+ value: '1',
+ },
+ ],
+ },
+ filter: '',
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(1);
+ const data = experimentResult.results[0] as RawResult;
+
+ expect(data.rawdata['data'][0]['t_value']).toBeCloseTo(18.477, 3);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/t-test-one-sample.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/t-test-one-sample.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a08e6fb3c9a4ce8332e09fc0a4b02b7cf89f2df7
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/t-test-one-sample.e2e-spec.ts
@@ -0,0 +1,89 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import { RawResult } from '../../../../models/result/raw-result.model';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `ttest-1s-${generateNumber()}`;
+ const algorithmId = 'TTEST_ONESAMPLE';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['righthippocampus', 'lefthippocampus'],
+ coVariables: ['gender', ' alzheimerbroadcategory'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ {
+ id: 'testvalue',
+ value: '3.0',
+ },
+ {
+ id: 'hypothesis',
+ value: 'different',
+ },
+ {
+ id: 'effectsize',
+ value: '1',
+ },
+ {
+ id: 'ci',
+ value: '1',
+ },
+ {
+ id: 'meandiff',
+ value: '1',
+ },
+ ],
+ },
+ filter: '',
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(1);
+ const data = experimentResult.results[0] as RawResult;
+
+ expect(data.rawdata['data'][0]['t_value']).toBeCloseTo(8.155, 3);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/t-test-paired.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/t-test-paired.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..dd2b971e8dcb5668faa917f1b1886efb1104359b
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/t-test-paired.e2e-spec.ts
@@ -0,0 +1,72 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import { RawResult } from '../../../../models/result/raw-result.model';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `ttest-paired-${generateNumber()}`;
+ const algorithmId = 'TTEST_PAIRED';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['lefthippocampus', 'righthippocampus'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ {
+ id: 'hypothesis',
+ value: 'different',
+ },
+ ],
+ },
+ filter: '',
+ };
+
+ describe('Integration Test for experiment API', () => {
+ it(`create ${algorithmId}`, async () => {
+ const experiment = await createExperiment(input, exaremeService);
+
+ expect(experiment).toBeTruthy();
+ expect(experiment?.status).toStrictEqual('pending');
+
+ expect(experiment?.id).toBeTruthy();
+
+ const experimentResult = await waitForResult(
+ experiment?.id ?? '',
+ exaremeService,
+ );
+
+ expect(experimentResult).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(1);
+ const data = experimentResult.results[0] as RawResult;
+
+ expect(data.rawdata['data'][0]['t_value']).toBeCloseTo(-63.2, 3);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/tests/e2e/two-way-anova.e2e-spec.ts b/api/src/engine/connectors/exareme/tests/e2e/two-way-anova.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7b616e3266ed5ad805c74297c512c22f4c20c734
--- /dev/null
+++ b/api/src/engine/connectors/exareme/tests/e2e/two-way-anova.e2e-spec.ts
@@ -0,0 +1,89 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { AppModule } from '../../../../../main/app.module';
+import { ENGINE_SERVICE } from '../../../../engine.constants';
+import { IEngineService } from '../../../../engine.interfaces';
+import { ExperimentCreateInput } from '../../../../models/experiment/input/experiment-create.input';
+import { RawResult } from '../../../../models/result/raw-result.model';
+import {
+ createExperiment,
+ generateNumber,
+ TEST_PATHOLOGIES,
+ TIMEOUT_DURATION_SECONDS,
+ waitForResult,
+} from '../../interfaces/test-utilities';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('ExaremeService', () => {
+ let exaremeService: IEngineService;
+
+ beforeEach(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ exaremeService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+ });
+ const modelSlug = `anova-2way-${generateNumber()}`;
+ const algorithmId = 'ANOVA';
+
+ const input: ExperimentCreateInput = {
+ name: modelSlug,
+ variables: ['lefthippocampus'],
+ coVariables: ['alzheimerbroadcategory'],
+ datasets: TEST_PATHOLOGIES.dementia.datasets
+ .filter((d) => d.code !== 'fake_longitudinal')
+ .map((d) => d.code),
+ domain: TEST_PATHOLOGIES.dementia.code,
+ algorithm: {
+ id: algorithmId,
+ type: 'string',
+ parameters: [
+ {
+ id: 'bins',
+ value: '40',
+ },
+ {
+ id: 'iterations_max_number',
+ value: '20',
+ },
+ {
+ id: 'sstype',
+ value: '2',
+ },
+ {
+ id: 'outputformat',
+ value: 'pfa',
+ },
+ {
+ id: 'design',
+ value: 'additive',
+ },
+ ],
+ },
+ 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).toBeTruthy();
+ expect(experimentResult.status).toStrictEqual('success');
+ expect(experimentResult.results.length).toBeGreaterThanOrEqual(1);
+ const data = experimentResult.results[0] as RawResult;
+
+ expect(data.rawdata['data'][0]['sumofsquares']).toBeCloseTo(34.196, 3);
+ });
+ });
+});
diff --git a/api/src/engine/connectors/exareme/transformations.ts b/api/src/engine/connectors/exareme/transformations.ts
index a57e677bf1e341a527f2c98c105376135c6a4339..07e59d977343342a6686f1f71ce936ee350cd7cd 100644
--- a/api/src/engine/connectors/exareme/transformations.ts
+++ b/api/src/engine/connectors/exareme/transformations.ts
@@ -5,16 +5,16 @@ import * as jsonata from 'jsonata'; // old import style needed due to 'export =
export const transformToAlgorithms = jsonata(`
(
- $params := ["y", "pathology", "dataset", "filter"];
+ $params := ["y", "pathology", "dataset", "filter", "x"];
$toArray := function($x) { $type($x) = 'array' ? $x : [$x]};
*.{
- 'name': name,
+ 'id': name,
'label': label,
'description': desc,
'parameters': $toArray(parameters[$not(name in $params)].{
- 'name': name,
+ 'id': name,
'description': desc,
'label': label,
'type': valueType,
@@ -30,30 +30,45 @@ export const transformToAlgorithms = jsonata(`
export const transformToExperiment = jsonata(`
(
- $params := ["y", "pathology", "dataset", "filter"];
+ $params := ["y", "pathology", "dataset", "filter", "x", "formula"];
+ $toArray := function($x) { $type($x) = 'array' ? $x : [$x]};
+ $convDate := function($v) { $type($v) = 'string' ? $toMillis($v) : $v };
+ $rp := function($v) {$replace($v, /(\\+|\\*|-)/, ',')};
+ $strSafe := function($v) { $type($v) = 'string' ? $v : "" };
+ $formula := $eval(algorithm.parameters[name = "formula"].value);
- {
+ ($ ~> | algorithm.parameters | {"name": name ? name : label } |){
"name": name,
- "uuid": uuid,
+ "id": uuid,
"author": createdBy,
"viewed": viewed,
"status": status,
- "createdAt": created,
- "finishedAt": finished,
+ "createdAt": $convDate(created),
+ "finishedAt": $convDate(finished),
"shared": shared,
- "updateAt": updated,
- "domains": algorithm.parameters[name = "pathology"].value,
- "variables": $split(algorithm.parameters[name = "y"].value, ','),
- "filter": algorithm.parameters[name = "filter"].value,
+ "updateAt": $convDate(updated),
+ "domain": algorithm.parameters[name = "pathology"].value,
"datasets": $split(algorithm.parameters[name = "dataset"].value, ','),
+ "variables": $split($rp(algorithm.parameters[name = "y"].value), ','),
+ "coVariables": $toArray($split($rp(algorithm.parameters[name = "x"].value), ',')),
+ "filterVariables": (algorithm.parameters[name = "filter"].value ~> $strSafe() ~> $match(/\\"id\\":\\"(\w*)\\"/)).groups,
+ "filter": algorithm.parameters[name = "filter"].value,
+ "formula": {
+ "transformations": $formula.single.{
+ "id": var_name,
+ "operation": unary_operation
+ }[],
+ "interactions" : $formula.interactions.[var1, var2][]
+ },
"algorithm": {
- "name": algorithm.name,
- "parameters" :
- algorithm.parameters[$not(name in $params)].({
- "name": name,
- "label": label,
- "value": value
- })
+ "id": algorithm.name,
+ "parameters" : $toArray(
+ algorithm.parameters[$not(name in $params)].({
+ "id": name,
+ "label": label,
+ "value": value
+ })
+ )
}
}
)
@@ -137,3 +152,57 @@ export const descriptiveSingleToTables = jsonata(`
]
)
`);
+
+export const dataROCToLineResult = jsonata(`
+({
+ "name": data.title.text,
+ "xAxis": {
+ "label": data.xAxis.title.text
+ },
+ "yAxis": {
+ "label": data.yAxis.title.text
+ },
+ "lines": [
+ {
+ "label": "ROC curve",
+ "x": data.series.data.$[0],
+ "y": data.series.data.$[1],
+ "type": 0
+ }
+ ]
+})
+`);
+
+export const dataToHeatmap = jsonata(`
+(
+ {
+ "name": data.title.text,
+ "xAxis": {
+ "categories": data.xAxis.categories,
+ "label": data.xAxis.label
+ },
+ "yAxis": {
+ "categories": data.yAxis.categories,
+ "label": data.yAxis.label
+ },
+ "matrix": $toMat(data.series.data)
+ }
+)
+`);
+
+dataToHeatmap.registerFunction(
+ 'toMat',
+ (a) => {
+ const matrix = [];
+
+ a.forEach(
+ (elem: { y: number | number; x: number | number; value: number }) => {
+ matrix[elem.y] = matrix[elem.y] ?? [];
+ matrix[elem.y][elem.x] = elem.value;
+ },
+ );
+
+ return matrix;
+ },
+ '<a<o>:a<a<n>>',
+);
diff --git a/api/src/engine/connectors/local/main.connector.ts b/api/src/engine/connectors/local/main.connector.ts
index cb472d927f571c9553c0115624a9981f2be653c6..003b3c8cc2927a84dda52f8efe97b7d44edb8ab8 100644
--- a/api/src/engine/connectors/local/main.connector.ts
+++ b/api/src/engine/connectors/local/main.connector.ts
@@ -33,18 +33,16 @@ export default class LocalService implements IEngineService {
throw new Error('Method not implemented.');
}
- getExperiment(uuid: string): Experiment | Promise<Experiment> {
+ getExperiment(id: string): Experiment | Promise<Experiment> {
throw new Error('Method not implemented.');
}
- removeExperiment(
- uuid: string,
- ): PartialExperiment | Promise<PartialExperiment> {
+ removeExperiment(id: string): PartialExperiment | Promise<PartialExperiment> {
throw new Error('Method not implemented.');
}
editExperient(
- uuid: string,
+ id: string,
expriment: ExperimentEditInput,
): Experiment | Promise<Experiment> {
throw new Error('Method not implemented.');
diff --git a/api/src/engine/engine.controller.ts b/api/src/engine/engine.controller.ts
index e56fa8e7ef75d1b50b233fa28f548129126f790f..a750538507388330a0407e4ef7f91700dc0b575b 100644
--- a/api/src/engine/engine.controller.ts
+++ b/api/src/engine/engine.controller.ts
@@ -30,19 +30,19 @@ export class EngineController {
return this.engineService.getExperiments();
}
- @Get('/experiments/:uuid')
- getExperiment(@Param('uuid') uuid: string): Observable<string> | string {
- return this.engineService.getExperimentREST(uuid);
+ @Get('/experiments/:id')
+ getExperiment(@Param('id') id: string): Observable<string> | string {
+ return this.engineService.getExperimentREST(id);
}
- @Delete('/experiments/:uuid')
- deleteExperiment(@Param('uuid') uuid: string): Observable<string> | string {
- return this.engineService.deleteExperiment(uuid);
+ @Delete('/experiments/:id')
+ deleteExperiment(@Param('id') id: string): Observable<string> | string {
+ return this.engineService.deleteExperiment(id);
}
- @Patch('/experiments/:uuid')
- editExperiment(@Param('uuid') uuid: string): Observable<string> | string {
- return this.engineService.editExperimentREST(uuid);
+ @Patch('/experiments/:id')
+ editExperiment(@Param('id') id: string): Observable<string> | string {
+ return this.engineService.editExperimentREST(id);
}
@Post('experiments/transient')
diff --git a/api/src/engine/engine.interfaces.ts b/api/src/engine/engine.interfaces.ts
index ec4fbc7fb43c1b163e3c28eb191162b0e0cf8337..a320765819458b30f430d84934b7e992af77459b 100644
--- a/api/src/engine/engine.interfaces.ts
+++ b/api/src/engine/engine.interfaces.ts
@@ -28,14 +28,12 @@ export interface IEngineService {
name: string,
): Promise<ListExperiments> | ListExperiments;
- getExperiment(uuid: string): Promise<Experiment> | Experiment;
+ getExperiment(id: string): Promise<Experiment> | Experiment;
- removeExperiment(
- uuid: string,
- ): Promise<PartialExperiment> | PartialExperiment;
+ removeExperiment(id: string): Promise<PartialExperiment> | PartialExperiment;
editExperient(
- uuid: string,
+ id: string,
expriment: ExperimentEditInput,
): Promise<Experiment> | Experiment;
@@ -46,11 +44,11 @@ export interface IEngineService {
getExperiments(): Observable<string> | string;
- getExperimentREST(uuid: string): Observable<string> | string;
+ getExperimentREST(id: string): Observable<string> | string;
- deleteExperiment(uuid: string): Observable<string> | string;
+ deleteExperiment(id: string): Observable<string> | string;
- editExperimentREST(uuid: string): Observable<string> | string;
+ editExperimentREST(id: string): Observable<string> | string;
startExperimentTransient(): Observable<string> | string;
diff --git a/api/src/engine/engine.module.ts b/api/src/engine/engine.module.ts
index 48442588a8d1a2c5120e99fa15d60e7da3c29739..6f8d33c6a63b40a9ac2c07a5bf3983ae0e148775 100644
--- a/api/src/engine/engine.module.ts
+++ b/api/src/engine/engine.module.ts
@@ -53,10 +53,11 @@ export class EngineModule {
const engine = new service.default(options, httpService, req);
return engine;
- } catch {
+ } catch (e) {
this.logger.error(
`There is a problem with the connector '${options.type}'`,
);
+ this.logger.verbose(e);
process.exit(); // We can't continue without an engine, shutdown the process...
}
}
diff --git a/api/src/engine/engine.resolver.ts b/api/src/engine/engine.resolver.ts
index 6e23ba38ca26d1129e51abb7cbba8d311cad67b9..ffed50e6467832491d03cf51cab35d6cc2292173 100644
--- a/api/src/engine/engine.resolver.ts
+++ b/api/src/engine/engine.resolver.ts
@@ -29,7 +29,7 @@ export class EngineResolver {
}
@Query(() => ListExperiments)
- async experiments(
+ async experimentList(
@Args('page', { nullable: true, defaultValue: 0 }) page: number,
@Args('name', { nullable: true, defaultValue: '' }) name: string,
) {
@@ -37,8 +37,8 @@ export class EngineResolver {
}
@Query(() => Experiment)
- async expriment(@Args('uuid') uuid: string) {
- return this.engineService.getExperiment(uuid);
+ async experiment(@Args('id') id: string) {
+ return this.engineService.getExperiment(id);
}
@Query(() => [Algorithm])
@@ -60,16 +60,14 @@ export class EngineResolver {
@Mutation(() => Experiment)
async editExperiment(
- @Args('uuid') uuid: string,
+ @Args('id') id: string,
@Args('data') experiment: ExperimentEditInput,
) {
- return this.engineService.editExperient(uuid, experiment);
+ return this.engineService.editExperient(id, experiment);
}
@Mutation(() => PartialExperiment)
- async removeExperiment(
- @Args('uuid') uuid: string,
- ): Promise<PartialExperiment> {
- return this.engineService.removeExperiment(uuid);
+ async removeExperiment(@Args('id') id: string): Promise<PartialExperiment> {
+ return this.engineService.removeExperiment(id);
}
}
diff --git a/api/src/engine/interceptors/headers.interceptor.ts b/api/src/engine/interceptors/headers.interceptor.ts
index 9b28e4953456de5d9bc66a390c9cf452cf45306f..8dddccb93815c21cb0f92c79bd97d4fb293bfd35 100644
--- a/api/src/engine/interceptors/headers.interceptor.ts
+++ b/api/src/engine/interceptors/headers.interceptor.ts
@@ -1,17 +1,35 @@
import { HttpService } from '@nestjs/axios';
-import { Injectable, NestInterceptor, CallHandler } from '@nestjs/common';
+import {
+ CallHandler,
+ HttpException,
+ Inject,
+ Injectable,
+ Logger,
+ NestInterceptor,
+} from '@nestjs/common';
import { GqlExecutionContext } from '@nestjs/graphql';
import { IncomingMessage } from 'http';
-import { Observable, tap } from 'rxjs';
+import { catchError, Observable, tap } from 'rxjs';
+import { ENGINE_MODULE_OPTIONS } from '../engine.constants';
+import { IEngineOptions } from '../engine.interfaces';
@Injectable()
export class HeadersInterceptor implements NestInterceptor {
- constructor(private httpService: HttpService) {}
+ private readonly logger: Logger;
+
+ constructor(
+ private httpService: HttpService,
+ @Inject(ENGINE_MODULE_OPTIONS) private readonly options: IEngineOptions,
+ ) {
+ // Logger name is the engine name
+ // HttpService will be used mostly by the engine (but it's not always true)
+ this.logger = new Logger(options.type);
+ }
intercept(context: GqlExecutionContext, next: CallHandler): Observable<any> {
// cleaner : add only the auth header (should find the name)
- const keys = ['cookie', 'x-xsrf-token'];
+ const keys = ['cookie', 'x-xsrf-token']; // should be a module parameter
let headers = {};
switch (context.getType()) {
@@ -29,7 +47,7 @@ export class HeadersInterceptor implements NestInterceptor {
}
}
- Object.keys(headers)
+ Object.keys(headers) // copy needed keys
.filter((key) => keys.includes(key))
.map((key) => key.toLowerCase())
.forEach((key) => {
@@ -37,8 +55,17 @@ export class HeadersInterceptor implements NestInterceptor {
});
return next.handle().pipe(
+ catchError((e) => {
+ if (!e.response.data || !e.response.status) return e;
+
+ this.logger.log(e.message);
+ this.logger.verbose(
+ `[Error ${e.response.status}] ${e.response.data.message}`,
+ );
+ throw new HttpException(e.response.data, e.response.status); // catch errors, maybe make it optional (module parameter)
+ }),
tap(() => {
- this.httpService.axiosRef.defaults.headers.common = {}; //cleaning request
+ this.httpService.axiosRef.defaults.headers.common = {}; // cleaning request
}),
);
}
diff --git a/api/src/engine/models/dataset.model.ts b/api/src/engine/models/dataset.model.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a15340b0281906705dfc12e32a8af5db4165a27f
--- /dev/null
+++ b/api/src/engine/models/dataset.model.ts
@@ -0,0 +1,8 @@
+import { Field, ObjectType } from '@nestjs/graphql';
+import { Entity } from './entity.model';
+
+@ObjectType()
+export class Dataset extends Entity {
+ @Field({ nullable: true, defaultValue: false })
+ isLongitudinal?: boolean;
+}
diff --git a/api/src/engine/models/domain.model.ts b/api/src/engine/models/domain.model.ts
index f5b8def42a318613b348040b2eccb3ea67a7aa29..1cfef22fb86343d0c521ada3e1e7c7ebc5e7e001 100644
--- a/api/src/engine/models/domain.model.ts
+++ b/api/src/engine/models/domain.model.ts
@@ -1,5 +1,5 @@
import { Field, ObjectType } from '@nestjs/graphql';
-import { Category } from './category.model';
+import { Dataset } from './dataset.model';
import { Entity } from './entity.model';
import { Group } from './group.model';
import { Variable } from './variable.model';
@@ -15,8 +15,8 @@ export class Domain extends Entity {
@Field(() => [Variable])
variables: Variable[];
- @Field(() => [Category])
- datasets: Category[];
+ @Field(() => [Dataset])
+ datasets: Dataset[];
@Field(() => Group)
rootGroup: Group;
diff --git a/api/src/engine/models/experiment/algorithm-parameter.model.ts b/api/src/engine/models/experiment/algorithm-parameter.model.ts
index d5db6bfc11634ae3ec054c4c6eef9a5441f74931..d934ebd9a19d08ab2a8b2d0ea1d84f4fa2f369eb 100644
--- a/api/src/engine/models/experiment/algorithm-parameter.model.ts
+++ b/api/src/engine/models/experiment/algorithm-parameter.model.ts
@@ -3,10 +3,10 @@ import { Field, ObjectType } from '@nestjs/graphql';
@ObjectType()
export class AlgorithmParameter {
@Field()
- name: string;
+ id: string;
- @Field(() => [String], { nullable: true })
- value?: string[];
+ @Field({ nullable: true })
+ value?: string;
@Field({ nullable: true })
label?: string;
diff --git a/api/src/engine/models/experiment/algorithm.model.ts b/api/src/engine/models/experiment/algorithm.model.ts
index ec26d747fc8019a29822bf673aa82b29162f5757..818b3c9d5c131a58625b3d724185cb6d87bc7827 100644
--- a/api/src/engine/models/experiment/algorithm.model.ts
+++ b/api/src/engine/models/experiment/algorithm.model.ts
@@ -4,7 +4,7 @@ import { AlgorithmParameter } from './algorithm-parameter.model';
@ObjectType()
export class Algorithm {
@Field()
- name: string;
+ id: string;
@Field(() => [AlgorithmParameter], { nullable: true, defaultValue: [] })
parameters?: AlgorithmParameter[];
diff --git a/api/src/engine/models/experiment/author.model.ts b/api/src/engine/models/experiment/author.model.ts
new file mode 100644
index 0000000000000000000000000000000000000000..0536a2e5a337e35f623dc9d649e817fa988dc13d
--- /dev/null
+++ b/api/src/engine/models/experiment/author.model.ts
@@ -0,0 +1,10 @@
+import { Field, ObjectType } from '@nestjs/graphql';
+
+@ObjectType()
+export class Author {
+ @Field({ nullable: true, defaultValue: '' })
+ username?: string;
+
+ @Field({ nullable: true, defaultValue: '' })
+ fullname?: string;
+}
diff --git a/api/src/engine/models/experiment/experiment.model.ts b/api/src/engine/models/experiment/experiment.model.ts
index 06e28b4b2e1c93e8dac7c6e7dc828c706f370c8a..eb757d64d9444f4c505705d3d6faa2b7e32c4d72 100644
--- a/api/src/engine/models/experiment/experiment.model.ts
+++ b/api/src/engine/models/experiment/experiment.model.ts
@@ -1,14 +1,36 @@
import { Field, ObjectType, PartialType } from '@nestjs/graphql';
import { ResultUnion } from '../result/common/result-union.model';
import { Algorithm } from './algorithm.model';
+import { Author } from './author.model';
+
+@ObjectType()
+export class Transformation {
+ @Field({ description: "Variable's id on which to apply the transformation" })
+ id: string;
+
+ @Field({ description: 'Transformation to apply' })
+ operation: string;
+}
+
+@ObjectType()
+export class Formula {
+ @Field(() => [Transformation], { nullable: true, defaultValue: [] })
+ transformations: Transformation[];
+
+ @Field(() => [[String]], { nullable: true, defaultValue: [] })
+ interactions: string[][];
+}
@ObjectType()
export class Experiment {
- @Field({ nullable: true })
- uuid?: string;
+ @Field()
+ id: string;
- @Field({ nullable: true, defaultValue: '' })
- author?: string;
+ @Field()
+ name: string;
+
+ @Field(() => Author, { nullable: true, defaultValue: '' })
+ author?: Author;
@Field({ nullable: true })
createdAt?: number;
@@ -43,11 +65,17 @@ export class Experiment {
@Field(() => [String])
variables: string[];
- @Field()
- algorithm: Algorithm;
+ @Field(() => [String], { nullable: true, defaultValue: [] })
+ coVariables?: string[];
+
+ @Field(() => [String], { nullable: true, defaultValue: [] })
+ filterVariables?: string[];
+
+ @Field(() => Formula, { nullable: true })
+ formula?: Formula;
@Field()
- name: string;
+ algorithm: Algorithm;
}
@ObjectType()
diff --git a/api/src/engine/models/experiment/input/algorithm-parameter.input.ts b/api/src/engine/models/experiment/input/algorithm-parameter.input.ts
index 8eb4cb26b5dade932440b6fef169275988d33b03..8cd3ec29ddfecb22c1574ea339cd96b4a010f79a 100644
--- a/api/src/engine/models/experiment/input/algorithm-parameter.input.ts
+++ b/api/src/engine/models/experiment/input/algorithm-parameter.input.ts
@@ -1,10 +1,25 @@
-import { Field, InputType } from '@nestjs/graphql';
+import { Field, InputType, registerEnumType } from '@nestjs/graphql';
+
+export enum ParamType {
+ STRING,
+ NUMBER,
+}
+
+registerEnumType(ParamType, {
+ name: 'ParamType',
+});
@InputType()
export class AlgorithmParamInput {
@Field()
- name: string;
+ id: string;
+
+ @Field(() => ParamType, {
+ nullable: true,
+ defaultValue: ParamType.STRING,
+ })
+ type?: ParamType;
- @Field(() => [String])
- value: string[];
+ @Field(() => String)
+ value: string;
}
diff --git a/api/src/engine/models/experiment/input/algorithm.input.ts b/api/src/engine/models/experiment/input/algorithm.input.ts
index 54d26b7686559c39b311cee5e5496bce530b0cf5..d87abd4561f975dbb9dfc00964f658265a340085 100644
--- a/api/src/engine/models/experiment/input/algorithm.input.ts
+++ b/api/src/engine/models/experiment/input/algorithm.input.ts
@@ -4,7 +4,7 @@ import { AlgorithmParamInput } from './algorithm-parameter.input';
@InputType()
export class AlgorithmInput {
@Field()
- name: string;
+ id: string;
@Field(() => [AlgorithmParamInput], { nullable: true, defaultValue: [] })
parameters: AlgorithmParamInput[];
diff --git a/api/src/engine/models/experiment/input/experiment-create.input.ts b/api/src/engine/models/experiment/input/experiment-create.input.ts
index b0b57cea85b17b0b49d4cbdf7b6cc12f21b71688..a34bb4c8a28c2ee456a6e88f44cdc6a87f4cd059 100644
--- a/api/src/engine/models/experiment/input/experiment-create.input.ts
+++ b/api/src/engine/models/experiment/input/experiment-create.input.ts
@@ -4,7 +4,7 @@ import { AlgorithmInput } from './algorithm.input';
@InputType()
export class FormulaTransformation {
@Field()
- name: string;
+ id: string;
@Field()
operation: string;
@@ -24,6 +24,9 @@ export class ExperimentCreateInput {
@Field(() => [String])
variables: string[];
+ @Field(() => [String], { nullable: true, defaultValue: [] })
+ coVariables?: string[];
+
@Field()
algorithm: AlgorithmInput;
@@ -31,8 +34,8 @@ export class ExperimentCreateInput {
name: string;
@Field(() => [FormulaTransformation], { nullable: true })
- transformations: FormulaTransformation[];
+ transformations?: FormulaTransformation[];
@Field(() => [[String]], { nullable: true })
- interactions: string[][];
+ interactions?: string[][];
}
diff --git a/api/src/engine/models/experiment/input/experiment-edit.input.ts b/api/src/engine/models/experiment/input/experiment-edit.input.ts
index d37deb1e8d008d746fda7214bb6890142b74a12a..30812416dea4bdb499226d44763790f9578f21a5 100644
--- a/api/src/engine/models/experiment/input/experiment-edit.input.ts
+++ b/api/src/engine/models/experiment/input/experiment-edit.input.ts
@@ -5,6 +5,9 @@ export class ExperimentEditInput {
@Field({ nullable: true })
name?: string;
+ @Field({ nullable: true })
+ shared?: boolean;
+
@Field({ nullable: true })
viewed?: boolean;
}
diff --git a/api/src/engine/models/result/common/result-union.model.ts b/api/src/engine/models/result/common/result-union.model.ts
index 2f56bb4d1f6ef577e9e836972f45dd59ede7fc28..bc4bb4a1472ea131fd8696da73d5c3d227c44a8f 100644
--- a/api/src/engine/models/result/common/result-union.model.ts
+++ b/api/src/engine/models/result/common/result-union.model.ts
@@ -19,10 +19,6 @@ export const ResultUnion = createUnionType({
return TableResult;
}
- if (value.rawdata) {
- return RawResult;
- }
-
if (value.groups) {
return GroupsResult;
}
@@ -31,10 +27,10 @@ export const ResultUnion = createUnionType({
return HeatMapResult;
}
- if (value.x) {
+ if (value.lines) {
return LineChartResult;
}
- return null;
+ return RawResult;
},
});
diff --git a/api/src/engine/models/result/heat-map-result.model.ts b/api/src/engine/models/result/heat-map-result.model.ts
index 267dc3c20201236e5d11ee1cbcbb6d6d89af15a7..8dd65ada27662536bffa7aeea6c8b78b0759c2fa 100644
--- a/api/src/engine/models/result/heat-map-result.model.ts
+++ b/api/src/engine/models/result/heat-map-result.model.ts
@@ -7,12 +7,12 @@ export class HeatMapResult extends Result {
@Field()
name: string;
- @Field(() => [[Number]])
- matrix: number[][];
+ @Field(() => ChartAxis, { nullable: true })
+ xAxis?: ChartAxis;
- @Field(() => ChartAxis)
- xAxis: ChartAxis;
+ @Field(() => ChartAxis, { nullable: true })
+ yAxis?: ChartAxis;
- @Field(() => ChartAxis)
- yAxis: ChartAxis;
+ @Field(() => [[Number]])
+ matrix: number[][];
}
diff --git a/api/src/engine/models/result/raw-result.model.ts b/api/src/engine/models/result/raw-result.model.ts
index 853362293bbfe6da230e487f8ea139ba36a16f3b..01528a5fd6dcbffe09d646bf7356ef87f18c200b 100644
--- a/api/src/engine/models/result/raw-result.model.ts
+++ b/api/src/engine/models/result/raw-result.model.ts
@@ -7,6 +7,6 @@ import { Result } from './common/result.model';
@ObjectType()
export class RawResult extends Result {
- @Field(() => GraphQLJSON)
- rawdata: unknown;
+ @Field(() => GraphQLJSON, { nullable: true, defaultValue: '' })
+ rawdata?: unknown;
}
diff --git a/api/src/engine/test/core.e2e-spec.ts b/api/src/engine/test/core.e2e-spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..bb35467dd1911ea2f88c8af9f0268218ddfdb8a5
--- /dev/null
+++ b/api/src/engine/test/core.e2e-spec.ts
@@ -0,0 +1,47 @@
+import { Test, TestingModule } from '@nestjs/testing';
+import { Domain } from 'src/engine/models/domain.model';
+import { AppModule } from '../../main/app.module';
+import { TIMEOUT_DURATION_SECONDS } from '../connectors/exareme/interfaces/test-utilities';
+import { ENGINE_SERVICE } from '../engine.constants';
+import { IEngineService } from '../engine.interfaces';
+
+jest.setTimeout(1000 * TIMEOUT_DURATION_SECONDS);
+
+describe('Engine service', () => {
+ let engineService: IEngineService;
+ let domains: Domain[];
+
+ beforeAll(async () => {
+ const moduleRef: TestingModule = await Test.createTestingModule({
+ imports: [AppModule],
+ }).compile();
+
+ engineService = await moduleRef.resolve<IEngineService>(ENGINE_SERVICE);
+
+ domains = await engineService.getDomains([]);
+ });
+
+ it('Get domains', async () => {
+ expect(domains).toBeTruthy();
+ expect(domains.length).toBeGreaterThanOrEqual(1);
+ });
+
+ it('Get datasets', async () => {
+ domains.forEach((domain) => {
+ expect(domain.datasets).toBeTruthy();
+ });
+ });
+
+ it('Get algorithms', async () => {
+ const algorithms = await engineService.getAlgorithms();
+ expect(algorithms).toBeTruthy();
+ expect(algorithms.length).toBeGreaterThanOrEqual(1);
+ });
+
+ it('Get groups', async () => {
+ domains.forEach((domain) => {
+ expect(domain.groups).toBeTruthy();
+ expect(domain.groups.length).toBeGreaterThanOrEqual(1);
+ });
+ });
+});
diff --git a/api/src/schema.gql b/api/src/schema.gql
index 1d30677261172d7d7fdc830d938d329d9b5f2d5d..854bd5ec152a379d4a5fcb3b94f6f6dbcf925d23 100644
--- a/api/src/schema.gql
+++ b/api/src/schema.gql
@@ -2,9 +2,10 @@
# THIS FILE WAS AUTOMATICALLY GENERATED (DO NOT MODIFY)
# ------------------------------------------------------
-type Category {
+type Dataset {
id: String!
label: String
+ isLongitudinal: Boolean
}
type Group {
@@ -17,6 +18,11 @@ type Group {
variables: [String!]
}
+type Category {
+ id: String!
+ label: String
+}
+
type Variable {
id: String!
label: String
@@ -32,13 +38,13 @@ type Domain {
description: String
groups: [Group!]!
variables: [Variable!]!
- datasets: [Category!]!
+ datasets: [Dataset!]!
rootGroup: Group!
}
type AlgorithmParameter {
- name: String!
- value: [String!]
+ id: String!
+ value: String
label: String
description: String
defaultValue: String
@@ -50,7 +56,7 @@ type AlgorithmParameter {
}
type Algorithm {
- name: String!
+ id: String!
parameters: [AlgorithmParameter!]
label: String
type: String
@@ -72,7 +78,7 @@ type TableResult {
}
type RawResult {
- rawdata: JSON!
+ rawdata: JSON
}
"""
@@ -86,9 +92,9 @@ type GroupsResult {
type HeatMapResult {
name: String!
+ xAxis: ChartAxis
+ yAxis: ChartAxis
matrix: [[Float!]!]!
- xAxis: ChartAxis!
- yAxis: ChartAxis!
}
type LineChartResult {
@@ -126,9 +132,28 @@ type Header {
type: String!
}
+type Author {
+ username: String
+ fullname: String
+}
+
+type Transformation {
+ """Variable's id on which to apply the transformation"""
+ id: String!
+
+ """Transformation to apply"""
+ operation: String!
+}
+
+type Formula {
+ transformations: [Transformation!]
+ interactions: [[String!]!]
+}
+
type Experiment {
- uuid: String
- author: String
+ id: String!
+ name: String!
+ author: Author
createdAt: Float
updateAt: Float
finishedAt: Float
@@ -140,13 +165,16 @@ type Experiment {
filter: String
domain: String!
variables: [String!]!
+ coVariables: [String!]
+ filterVariables: [String!]
+ formula: Formula
algorithm: Algorithm!
- name: String!
}
type PartialExperiment {
- uuid: String
- author: String
+ id: String
+ name: String
+ author: Author
createdAt: Float
updateAt: Float
finishedAt: Float
@@ -158,8 +186,10 @@ type PartialExperiment {
filter: String
domain: String
variables: [String!]
+ coVariables: [String!]
+ filterVariables: [String!]
+ formula: Formula
algorithm: Algorithm
- name: String
}
type ListExperiments {
@@ -171,15 +201,15 @@ type ListExperiments {
type Query {
domains(ids: [String!] = []): [Domain!]!
- experiments(name: String = "", page: Float = 0): ListExperiments!
- expriment(uuid: String!): Experiment!
+ experimentList(name: String = "", page: Float = 0): ListExperiments!
+ experiment(id: String!): Experiment!
algorithms: [Algorithm!]!
}
type Mutation {
createExperiment(isTransient: Boolean = false, data: ExperimentCreateInput!): Experiment!
- editExperiment(data: ExperimentEditInput!, uuid: String!): Experiment!
- removeExperiment(uuid: String!): PartialExperiment!
+ editExperiment(data: ExperimentEditInput!, id: String!): Experiment!
+ removeExperiment(id: String!): PartialExperiment!
}
input ExperimentCreateInput {
@@ -187,6 +217,7 @@ input ExperimentCreateInput {
filter: String
domain: String!
variables: [String!]!
+ coVariables: [String!] = []
algorithm: AlgorithmInput!
name: String!
transformations: [FormulaTransformation!]
@@ -194,22 +225,29 @@ input ExperimentCreateInput {
}
input AlgorithmInput {
- name: String!
+ id: String!
parameters: [AlgorithmParamInput!] = []
type: String!
}
input AlgorithmParamInput {
- name: String!
- value: [String!]!
+ id: String!
+ type: ParamType = STRING
+ value: String!
+}
+
+enum ParamType {
+ STRING
+ NUMBER
}
input FormulaTransformation {
- name: String!
+ id: String!
operation: String!
}
input ExperimentEditInput {
name: String
+ shared: Boolean
viewed: Boolean
}
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',
+ },
+ };
+};