diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cd06272d937f09989f48cacde2eb67761be9c214..b14587cde6c56a5749d5082d741a619704e006d1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -16,17 +16,6 @@ workflow:
# Pipeline start
# =============================================================================
-# Run the unit tests
-testing:
- image: node:22-alpine
- stage: validate
- rules:
- - changes:
- - src/**/*
- script:
- - npm ci
- - npm test
-
# Validate the fasta files if they have changed
validate-fasta-files:
image: node:22-alpine
diff --git a/package-lock.json b/package-lock.json
index 7b789b2a249c7ec5d60c55fd54a3c6c43281fa32..d8ca428b5e9cef3587ce14a4dce059676341825d 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -37,7 +37,6 @@
"rollup-plugin-gzip": "^4.0.1",
"typescript": "^5.7.3",
"vite": "^6.1.0",
- "vitest": "^3.0.5",
"vue-tsc": "^2.2.0"
}
},
@@ -1253,129 +1252,6 @@
"vue": "^3.2.25"
}
},
- "node_modules/@vitest/expect": {
- "version": "3.0.5",
- "resolved": "https://registry.npmjs.org/@vitest/expect/-/expect-3.0.5.tgz",
- "integrity": "sha512-nNIOqupgZ4v5jWuQx2DSlHLEs7Q4Oh/7AYwNyE+k0UQzG7tSmjPXShUikn1mpNGzYEN2jJbTvLejwShMitovBA==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "@vitest/spy": "3.0.5",
- "@vitest/utils": "3.0.5",
- "chai": "^5.1.2",
- "tinyrainbow": "^2.0.0"
- },
- "funding": {
- "url": "https://opencollective.com/vitest"
- }
- },
- "node_modules/@vitest/mocker": {
- "version": "3.0.5",
- "resolved": "https://registry.npmjs.org/@vitest/mocker/-/mocker-3.0.5.tgz",
- "integrity": "sha512-CLPNBFBIE7x6aEGbIjaQAX03ZZlBMaWwAjBdMkIf/cAn6xzLTiM3zYqO/WAbieEjsAZir6tO71mzeHZoodThvw==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "@vitest/spy": "3.0.5",
- "estree-walker": "^3.0.3",
- "magic-string": "^0.30.17"
- },
- "funding": {
- "url": "https://opencollective.com/vitest"
- },
- "peerDependencies": {
- "msw": "^2.4.9",
- "vite": "^5.0.0 || ^6.0.0"
- },
- "peerDependenciesMeta": {
- "msw": {
- "optional": true
- },
- "vite": {
- "optional": true
- }
- }
- },
- "node_modules/@vitest/mocker/node_modules/estree-walker": {
- "version": "3.0.3",
- "resolved": "https://registry.npmjs.org/estree-walker/-/estree-walker-3.0.3.tgz",
- "integrity": "sha512-7RUKfXgSMMkzt6ZuXmqapOurLGPPfgj6l9uRZ7lRGolvk0y2yocc35LdcxKC5PQZdn2DMqioAQ2NoWcrTKmm6g==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "@types/estree": "^1.0.0"
- }
- },
- "node_modules/@vitest/pretty-format": {
- "version": "3.0.5",
- "resolved": "https://registry.npmjs.org/@vitest/pretty-format/-/pretty-format-3.0.5.tgz",
- "integrity": "sha512-CjUtdmpOcm4RVtB+up8r2vVDLR16Mgm/bYdkGFe3Yj/scRfCpbSi2W/BDSDcFK7ohw8UXvjMbOp9H4fByd/cOA==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "tinyrainbow": "^2.0.0"
- },
- "funding": {
- "url": "https://opencollective.com/vitest"
- }
- },
- "node_modules/@vitest/runner": {
- "version": "3.0.5",
- "resolved": "https://registry.npmjs.org/@vitest/runner/-/runner-3.0.5.tgz",
- "integrity": "sha512-BAiZFityFexZQi2yN4OX3OkJC6scwRo8EhRB0Z5HIGGgd2q+Nq29LgHU/+ovCtd0fOfXj5ZI6pwdlUmC5bpi8A==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "@vitest/utils": "3.0.5",
- "pathe": "^2.0.2"
- },
- "funding": {
- "url": "https://opencollective.com/vitest"
- }
- },
- "node_modules/@vitest/snapshot": {
- "version": "3.0.5",
- "resolved": "https://registry.npmjs.org/@vitest/snapshot/-/snapshot-3.0.5.tgz",
- "integrity": "sha512-GJPZYcd7v8QNUJ7vRvLDmRwl+a1fGg4T/54lZXe+UOGy47F9yUfE18hRCtXL5aHN/AONu29NGzIXSVFh9K0feA==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "@vitest/pretty-format": "3.0.5",
- "magic-string": "^0.30.17",
- "pathe": "^2.0.2"
- },
- "funding": {
- "url": "https://opencollective.com/vitest"
- }
- },
- "node_modules/@vitest/spy": {
- "version": "3.0.5",
- "resolved": "https://registry.npmjs.org/@vitest/spy/-/spy-3.0.5.tgz",
- "integrity": "sha512-5fOzHj0WbUNqPK6blI/8VzZdkBlQLnT25knX0r4dbZI9qoZDf3qAdjoMmDcLG5A83W6oUUFJgUd0EYBc2P5xqg==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "tinyspy": "^3.0.2"
- },
- "funding": {
- "url": "https://opencollective.com/vitest"
- }
- },
- "node_modules/@vitest/utils": {
- "version": "3.0.5",
- "resolved": "https://registry.npmjs.org/@vitest/utils/-/utils-3.0.5.tgz",
- "integrity": "sha512-N9AX0NUoUtVwKwy21JtwzaqR5L5R5A99GAbrHfCCXK1lp593i/3AZAXhSP43wRQuxYsflrdzEfXZFo1reR1Nkg==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "@vitest/pretty-format": "3.0.5",
- "loupe": "^3.1.2",
- "tinyrainbow": "^2.0.0"
- },
- "funding": {
- "url": "https://opencollective.com/vitest"
- }
- },
"node_modules/@volar/language-core": {
"version": "2.4.11",
"resolved": "https://registry.npmjs.org/@volar/language-core/-/language-core-2.4.11.tgz",
@@ -1692,16 +1568,6 @@
"node": ">= 8"
}
},
- "node_modules/assertion-error": {
- "version": "2.0.1",
- "resolved": "https://registry.npmjs.org/assertion-error/-/assertion-error-2.0.1.tgz",
- "integrity": "sha512-Izi8RQcffqCeNVgFigKli1ssklIbpHnCYc6AknXGYoB6grJqyeby7jv12JUQgmTAnIDnbck1uxksT4dzN3PWBA==",
- "dev": true,
- "license": "MIT",
- "engines": {
- "node": ">=12"
- }
- },
"node_modules/asynckit": {
"version": "0.4.0",
"resolved": "https://registry.npmjs.org/asynckit/-/asynckit-0.4.0.tgz",
@@ -1907,16 +1773,6 @@
"ieee754": "^1.2.1"
}
},
- "node_modules/cac": {
- "version": "6.7.14",
- "resolved": "https://registry.npmjs.org/cac/-/cac-6.7.14.tgz",
- "integrity": "sha512-b6Ilus+c3RrdDk+JhLKUAQfzzgLEPy6wcXqS7f/xe1EETvsDP6GORG7SFuOs6cID5YkqchW/LXZbX5bc8j7ZcQ==",
- "dev": true,
- "license": "MIT",
- "engines": {
- "node": ">=8"
- }
- },
"node_modules/call-bind-apply-helpers": {
"version": "1.0.1",
"resolved": "https://registry.npmjs.org/call-bind-apply-helpers/-/call-bind-apply-helpers-1.0.1.tgz",
@@ -1979,23 +1835,6 @@
],
"license": "CC-BY-4.0"
},
- "node_modules/chai": {
- "version": "5.1.2",
- "resolved": "https://registry.npmjs.org/chai/-/chai-5.1.2.tgz",
- "integrity": "sha512-aGtmf24DW6MLHHG5gCx4zaI3uBq3KRtxeVs0DjFH6Z0rDNbsvTxFASFvdj79pxjxZ8/5u3PIiN3IwEIQkiiuPw==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "assertion-error": "^2.0.1",
- "check-error": "^2.1.1",
- "deep-eql": "^5.0.1",
- "loupe": "^3.1.0",
- "pathval": "^2.0.0"
- },
- "engines": {
- "node": ">=12"
- }
- },
"node_modules/chalk": {
"version": "4.1.2",
"resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.2.tgz",
@@ -2024,16 +1863,6 @@
"node": ">=8"
}
},
- "node_modules/check-error": {
- "version": "2.1.1",
- "resolved": "https://registry.npmjs.org/check-error/-/check-error-2.1.1.tgz",
- "integrity": "sha512-OAlb+T7V4Op9OwdkjmguYRqncdlx5JiofwOAUkmTF+jNdHwzTaTs4sRAGpzLF3oOz5xAyDGrPgeIDFQmDOTiJw==",
- "dev": true,
- "license": "MIT",
- "engines": {
- "node": ">= 16"
- }
- },
"node_modules/chokidar": {
"version": "3.5.3",
"resolved": "https://registry.npmjs.org/chokidar/-/chokidar-3.5.3.tgz",
@@ -2429,16 +2258,6 @@
}
}
},
- "node_modules/deep-eql": {
- "version": "5.0.2",
- "resolved": "https://registry.npmjs.org/deep-eql/-/deep-eql-5.0.2.tgz",
- "integrity": "sha512-h5k/5U50IJJFpzfL6nO9jaaumfjO/f2NjK/oYB2Djzm4p9L+3T9qWpZqZ2hAbLPuuYq9wrU08WQyBTL5GbPk5Q==",
- "dev": true,
- "license": "MIT",
- "engines": {
- "node": ">=6"
- }
- },
"node_modules/delayed-stream": {
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/delayed-stream/-/delayed-stream-1.0.0.tgz",
@@ -2620,13 +2439,6 @@
"node": ">= 0.4"
}
},
- "node_modules/es-module-lexer": {
- "version": "1.6.0",
- "resolved": "https://registry.npmjs.org/es-module-lexer/-/es-module-lexer-1.6.0.tgz",
- "integrity": "sha512-qqnD1yMU6tk/jnaMosogGySTZP8YtUgAffA9nMN+E/rjxcfRQ6IEk7IiozUjgxKoFHBGjTLnrHB/YC45r/59EQ==",
- "dev": true,
- "license": "MIT"
- },
"node_modules/es-object-atoms": {
"version": "1.1.1",
"resolved": "https://registry.npmjs.org/es-object-atoms/-/es-object-atoms-1.1.1.tgz",
@@ -2717,16 +2529,6 @@
"node": ">=0.8.x"
}
},
- "node_modules/expect-type": {
- "version": "1.1.0",
- "resolved": "https://registry.npmjs.org/expect-type/-/expect-type-1.1.0.tgz",
- "integrity": "sha512-bFi65yM+xZgk+u/KRIpekdSYkTB5W1pEf0Lt8Q8Msh7b+eQ7LXVtIB1Bkm4fvclDEL1b2CZkMhv2mOeF8tMdkA==",
- "dev": true,
- "license": "Apache-2.0",
- "engines": {
- "node": ">=12.0.0"
- }
- },
"node_modules/fast-copy": {
"version": "3.0.2",
"resolved": "https://registry.npmjs.org/fast-copy/-/fast-copy-3.0.2.tgz",
@@ -3328,13 +3130,6 @@
"integrity": "sha512-xfBaXQd9ryd9dlSDvnvI0lvxfLJlYAZzXomUYzLKtUeOQvOP5piqAWuGtrhWeqaXK9hhoM/iyJc5AV+XfsX3HQ==",
"dev": true
},
- "node_modules/loupe": {
- "version": "3.1.3",
- "resolved": "https://registry.npmjs.org/loupe/-/loupe-3.1.3.tgz",
- "integrity": "sha512-kkIp7XSkP78ZxJEsSxW3712C6teJVoeHHwgo9zJ380de7IYyJ2ISlxojcH2pC5OFLewESmnRi/+XCDIEEVyoug==",
- "dev": true,
- "license": "MIT"
- },
"node_modules/lru-cache": {
"version": "11.0.1",
"resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-11.0.1.tgz",
@@ -3706,23 +3501,6 @@
"url": "https://github.com/sponsors/isaacs"
}
},
- "node_modules/pathe": {
- "version": "2.0.3",
- "resolved": "https://registry.npmjs.org/pathe/-/pathe-2.0.3.tgz",
- "integrity": "sha512-WUjGcAqP1gQacoQe+OBJsFA7Ld4DyXuUIjZ5cc75cLHvJ7dtNsTugphxIADwspS+AraAUePCKrSVtPLFj/F88w==",
- "dev": true,
- "license": "MIT"
- },
- "node_modules/pathval": {
- "version": "2.0.0",
- "resolved": "https://registry.npmjs.org/pathval/-/pathval-2.0.0.tgz",
- "integrity": "sha512-vE7JKRyES09KiunauX7nd2Q9/L7lhok4smP9RZTDeD4MVs72Dp2qNFVz39Nz5a0FVEW0BJR6C0DYrq6unoziZA==",
- "dev": true,
- "license": "MIT",
- "engines": {
- "node": ">= 14.16"
- }
- },
"node_modules/perfect-debounce": {
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/perfect-debounce/-/perfect-debounce-1.0.0.tgz",
@@ -4689,13 +4467,6 @@
"url": "https://github.com/sponsors/ljharb"
}
},
- "node_modules/siginfo": {
- "version": "2.0.0",
- "resolved": "https://registry.npmjs.org/siginfo/-/siginfo-2.0.0.tgz",
- "integrity": "sha512-ybx0WO1/8bSBLEWXZvEd7gMW3Sn3JFlW3TvX1nREbDLRNQNaeNN8WK0meBwPdAaOI7TtRRRJn/Es1zhrrCHu7g==",
- "dev": true,
- "license": "ISC"
- },
"node_modules/signal-exit": {
"version": "4.1.0",
"resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-4.1.0.tgz",
@@ -4763,13 +4534,6 @@
"node": ">= 10.x"
}
},
- "node_modules/stackback": {
- "version": "0.0.2",
- "resolved": "https://registry.npmjs.org/stackback/-/stackback-0.0.2.tgz",
- "integrity": "sha512-1XMJE5fQo1jGH6Y/7ebnwPOBEkIEnT4QF32d5R1+VXdXveM0IBMJt8zfaxX1P3QhVwrYe+576+jkANtSS2mBbw==",
- "dev": true,
- "license": "MIT"
- },
"node_modules/statuses": {
"version": "2.0.1",
"resolved": "https://registry.npmjs.org/statuses/-/statuses-2.0.1.tgz",
@@ -4779,13 +4543,6 @@
"node": ">= 0.8"
}
},
- "node_modules/std-env": {
- "version": "3.8.0",
- "resolved": "https://registry.npmjs.org/std-env/-/std-env-3.8.0.tgz",
- "integrity": "sha512-Bc3YwwCB+OzldMxOXJIIvC6cPRWr/LxOp48CdQTOkPyk/t4JWWJbrilwBd7RJzKV8QW7tJkcgAmeuLLJugl5/w==",
- "dev": true,
- "license": "MIT"
- },
"node_modules/string_decoder": {
"version": "1.3.0",
"resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.3.0.tgz",
@@ -4934,50 +4691,6 @@
"real-require": "^0.2.0"
}
},
- "node_modules/tinybench": {
- "version": "2.9.0",
- "resolved": "https://registry.npmjs.org/tinybench/-/tinybench-2.9.0.tgz",
- "integrity": "sha512-0+DUvqWMValLmha6lr4kD8iAMK1HzV0/aKnCtWb9v9641TnP/MFb7Pc2bxoxQjTXAErryXVgUOfv2YqNllqGeg==",
- "dev": true,
- "license": "MIT"
- },
- "node_modules/tinyexec": {
- "version": "0.3.2",
- "resolved": "https://registry.npmjs.org/tinyexec/-/tinyexec-0.3.2.tgz",
- "integrity": "sha512-KQQR9yN7R5+OSwaK0XQoj22pwHoTlgYqmUscPYoknOoWCWfj/5/ABTMRi69FrKU5ffPVh5QcFikpWJI/P1ocHA==",
- "dev": true,
- "license": "MIT"
- },
- "node_modules/tinypool": {
- "version": "1.0.2",
- "resolved": "https://registry.npmjs.org/tinypool/-/tinypool-1.0.2.tgz",
- "integrity": "sha512-al6n+QEANGFOMf/dmUMsuS5/r9B06uwlyNjZZql/zv8J7ybHCgoihBNORZCY2mzUuAnomQa2JdhyHKzZxPCrFA==",
- "dev": true,
- "license": "MIT",
- "engines": {
- "node": "^18.0.0 || >=20.0.0"
- }
- },
- "node_modules/tinyrainbow": {
- "version": "2.0.0",
- "resolved": "https://registry.npmjs.org/tinyrainbow/-/tinyrainbow-2.0.0.tgz",
- "integrity": "sha512-op4nsTR47R6p0vMUUoYl/a+ljLFVtlfaXkLQmqfLR1qHma1h/ysYk4hEXZ880bf2CYgTskvTa/e196Vd5dDQXw==",
- "dev": true,
- "license": "MIT",
- "engines": {
- "node": ">=14.0.0"
- }
- },
- "node_modules/tinyspy": {
- "version": "3.0.2",
- "resolved": "https://registry.npmjs.org/tinyspy/-/tinyspy-3.0.2.tgz",
- "integrity": "sha512-n1cw8k1k0x4pgA2+9XrOkFydTerNcJ1zWCO5Nn9scWHTD+5tp8dghT2x1uduQePZTZgd3Tupf+x9BxJjeJi77Q==",
- "dev": true,
- "license": "MIT",
- "engines": {
- "node": ">=14.0.0"
- }
- },
"node_modules/to-regex-range": {
"version": "5.0.1",
"resolved": "https://registry.npmjs.org/to-regex-range/-/to-regex-range-5.0.1.tgz",
@@ -5189,99 +4902,6 @@
}
}
},
- "node_modules/vite-node": {
- "version": "3.0.5",
- "resolved": "https://registry.npmjs.org/vite-node/-/vite-node-3.0.5.tgz",
- "integrity": "sha512-02JEJl7SbtwSDJdYS537nU6l+ktdvcREfLksk/NDAqtdKWGqHl+joXzEubHROmS3E6pip+Xgu2tFezMu75jH7A==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "cac": "^6.7.14",
- "debug": "^4.4.0",
- "es-module-lexer": "^1.6.0",
- "pathe": "^2.0.2",
- "vite": "^5.0.0 || ^6.0.0"
- },
- "bin": {
- "vite-node": "vite-node.mjs"
- },
- "engines": {
- "node": "^18.0.0 || ^20.0.0 || >=22.0.0"
- },
- "funding": {
- "url": "https://opencollective.com/vitest"
- }
- },
- "node_modules/vitest": {
- "version": "3.0.5",
- "resolved": "https://registry.npmjs.org/vitest/-/vitest-3.0.5.tgz",
- "integrity": "sha512-4dof+HvqONw9bvsYxtkfUp2uHsTN9bV2CZIi1pWgoFpL1Lld8LA1ka9q/ONSsoScAKG7NVGf2stJTI7XRkXb2Q==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "@vitest/expect": "3.0.5",
- "@vitest/mocker": "3.0.5",
- "@vitest/pretty-format": "^3.0.5",
- "@vitest/runner": "3.0.5",
- "@vitest/snapshot": "3.0.5",
- "@vitest/spy": "3.0.5",
- "@vitest/utils": "3.0.5",
- "chai": "^5.1.2",
- "debug": "^4.4.0",
- "expect-type": "^1.1.0",
- "magic-string": "^0.30.17",
- "pathe": "^2.0.2",
- "std-env": "^3.8.0",
- "tinybench": "^2.9.0",
- "tinyexec": "^0.3.2",
- "tinypool": "^1.0.2",
- "tinyrainbow": "^2.0.0",
- "vite": "^5.0.0 || ^6.0.0",
- "vite-node": "3.0.5",
- "why-is-node-running": "^2.3.0"
- },
- "bin": {
- "vitest": "vitest.mjs"
- },
- "engines": {
- "node": "^18.0.0 || ^20.0.0 || >=22.0.0"
- },
- "funding": {
- "url": "https://opencollective.com/vitest"
- },
- "peerDependencies": {
- "@edge-runtime/vm": "*",
- "@types/debug": "^4.1.12",
- "@types/node": "^18.0.0 || ^20.0.0 || >=22.0.0",
- "@vitest/browser": "3.0.5",
- "@vitest/ui": "3.0.5",
- "happy-dom": "*",
- "jsdom": "*"
- },
- "peerDependenciesMeta": {
- "@edge-runtime/vm": {
- "optional": true
- },
- "@types/debug": {
- "optional": true
- },
- "@types/node": {
- "optional": true
- },
- "@vitest/browser": {
- "optional": true
- },
- "@vitest/ui": {
- "optional": true
- },
- "happy-dom": {
- "optional": true
- },
- "jsdom": {
- "optional": true
- }
- }
- },
"node_modules/vscode-uri": {
"version": "3.0.8",
"resolved": "https://registry.npmjs.org/vscode-uri/-/vscode-uri-3.0.8.tgz",
@@ -5376,23 +4996,6 @@
"node": ">= 8"
}
},
- "node_modules/why-is-node-running": {
- "version": "2.3.0",
- "resolved": "https://registry.npmjs.org/why-is-node-running/-/why-is-node-running-2.3.0.tgz",
- "integrity": "sha512-hUrmaWBdVDcxvYqnyh09zunKzROWjbZTiNy8dBEjkS7ehEDQibXJ7XvlmtbwuTclUiIyN+CyXQD4Vmko8fNm8w==",
- "dev": true,
- "license": "MIT",
- "dependencies": {
- "siginfo": "^2.0.0",
- "stackback": "0.0.2"
- },
- "bin": {
- "why-is-node-running": "cli.js"
- },
- "engines": {
- "node": ">=8"
- }
- },
"node_modules/wrap-ansi": {
"version": "7.0.0",
"resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz",
diff --git a/package.json b/package.json
index d2046610b82c220d69bdcdffdea1db0c4eb12498..1db9e6fecd006fa3512b978b7efd77e4353b77ee 100644
--- a/package.json
+++ b/package.json
@@ -9,7 +9,6 @@
"dev": "concurrently -n Client,Server -c '#325D79,#45ADA8' 'npm:dev:client' 'npm:dev:server'",
"dev:client": "vite",
"dev:server": "nodemon --use-strict src/server/app.js | pino-pretty -t 'yyyy-mm-dd HH:MM:ss'",
- "test": "NODE_ENV='production' vitest",
"build": "vue-tsc && vite build",
"build:db": "node src/scripts/buildDatabase.js",
"stats": "node src/scripts/displayStatistics",
@@ -57,7 +56,6 @@
"rollup-plugin-gzip": "^4.0.1",
"typescript": "^5.7.3",
"vite": "^6.1.0",
- "vitest": "^3.0.5",
"vue-tsc": "^2.2.0"
}
}
diff --git a/src/server/config/env.test.js b/src/server/config/env.test.js
deleted file mode 100644
index f026aa22e75fd81a8d0c3614ae0471a1e80adde3..0000000000000000000000000000000000000000
--- a/src/server/config/env.test.js
+++ /dev/null
@@ -1,69 +0,0 @@
-// ABSD
-// Copyright (C) 2023 Institut Pasteur
-//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-import { describe, expect, test } from 'vitest'
-import serverConfig from './env'
-
-describe('Server env config', () => {
- test('Config should exists', () => {
- expect(serverConfig).toBeDefined()
- })
-
- test('Config should have all and only the defined properties', () => {
- const envVariables = Object.keys(serverConfig).sort()
- expect(envVariables).toStrictEqual([
- "ABSD_DB_HOST",
- "ABSD_DB_NAME",
- "ABSD_DB_PORT",
- "ABSD_SERVER_HOST",
- "ABSD_SERVER_PORT",
- "ABSD_SERVER_PROXY",
- "NODE_ENV",
- ])
- })
-
- test('ABSD_DB_HOST should be a string', () => {
- expect(serverConfig.ABSD_DB_HOST).toBeTypeOf('string')
- })
-
- test('ABSD_DB_NAME should be a string', () => {
- expect(serverConfig.ABSD_DB_NAME).toBeTypeOf('string')
- })
-
- test('ABSD_DB_PORT should be a positive integer', () => {
- expect(serverConfig.ABSD_DB_PORT).toBeTypeOf('number')
- expect(serverConfig.ABSD_DB_PORT).toBeGreaterThan(0)
- expect(serverConfig.ABSD_DB_PORT % 1).toBe(0)
- })
-
- test('ABSD_SERVER_HOST should be a string', () => {
- expect(serverConfig.ABSD_SERVER_HOST).toBeTypeOf('string')
- })
-
- test('ABSD_SERVER_PORT should be a positive integer', () => {
- expect(serverConfig.ABSD_SERVER_PORT).toBeTypeOf('number')
- expect(serverConfig.ABSD_SERVER_PORT).toBeGreaterThan(0)
- expect(serverConfig.ABSD_SERVER_PORT % 1).toBe(0)
- })
-
- test('ABSD_SERVER_PROXY should be a boolean', () => {
- expect(serverConfig.ABSD_SERVER_PROXY).toBeTypeOf('boolean')
- })
-
- test('NODE_ENV should be either development or production', () => {
- expect(serverConfig.NODE_ENV).toBeOneOf(['development', 'production'])
- })
-})
diff --git a/src/server/models/Antibody.test.js b/src/server/models/Antibody.test.js
deleted file mode 100644
index 7dd24c344dbdc7f03a9a42db11e63f6cf29c4119..0000000000000000000000000000000000000000
--- a/src/server/models/Antibody.test.js
+++ /dev/null
@@ -1,140 +0,0 @@
-// ABSD
-// Copyright (C) 2023 Institut Pasteur
-//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-import { describe, expect, test } from "vitest"
-import { Antibody } from "./Antibody"
-
-describe('Antibody class', () => {
- test('should be a class', () => {
- const antibody = new Antibody()
- expect(antibody).toBeInstanceOf(Antibody)
- })
-
- test('should define the static method "listSources"', () => {
- expect(Antibody.listSources).toBeInstanceOf(Function)
- })
-
- test('should define the static method "listSegments"', () => {
- expect(Antibody.listSegments).toBeInstanceOf(Function)
- })
-
- test('should define the static method "generateHashId"', () => {
- expect(Antibody.generateHashId).toBeInstanceOf(Function)
- })
-
- test('should define the static method "toFasta"', () => {
- expect(Antibody.toFasta).toBeInstanceOf(Function)
- })
-
- test('should define the static method "toString"', () => {
- expect(Antibody.toString).toBeInstanceOf(Function)
- })
-})
-
-describe('Antibody class methods', () => {
- const antibody = {
- "id": "368.22.A.0062",
- "species": "Homo sapiens",
- "hashId": "53775feae7c2d86939d15177e0b963e20504141de8601e28ab701f9f4fe9d3a2",
- "lightChain": {
- "headers": [
- {
- "id": "368.22.A.0062",
- "vGeneSegment": "IGLV4",
- "source": "CoV-AbDab",
- "header": "368.22.A.0062_B-cells SARS-CoV2 Human Patient_human_light_"
- },
- {
- "id": "SRR17729722",
- "vGeneSegment": "IGLV4",
- "source": "PairedNGS",
- "header": "PRJNA777934|SRR17729722|human|GCTGCAGGTACCTACA|IGHV3_30*04,IGHD4_23*01,IGHJ3*02,IGHG1|IGLV4_69*01,IGLJ1*01,IGLC1|AKVEGGNYVGAFDV|QTWGTGIHV_light"
- },
- {
- "id": "SRR17778139",
- "vGeneSegment": "IGLV4",
- "source": "PairedNGS",
- "header": "PRJNA777934|SRR17778139|human|GCTGCAGGTACCTACA|IGHV3_30*04,IGHD4_23*01,IGHJ3*02|IGLV4_69*01,IGLJ1*01,IGLC1|AKVEGGNYVGAFDV|QTWGTGIHV_light"
- }
- ],
- "sequence": "QLVLTQSPSASASLGASVKLTCTLSSGHSSYAIAWHQQQPEKGPRYLMKLNSDGSHSEGDGIPDRFSGSSSGAERYLTISSLQSEDEADYYCQTWGTGIHVFGTGTKVTVL",
- "rawFasta": "368.22.A.0062|||368.22.A.0062_B-cells SARS-CoV2 Human Patient_human_light_;368.22.A.0062;IGLV4;CoV-AbDab|||PRJNA777934|SRR17729722|human|GCTGCAGGTACCTACA|IGHV3_30*04,IGHD4_23*01,IGHJ3*02,IGHG1|IGLV4_69*01,IGLJ1*01,IGLC1|AKVEGGNYVGAFDV|QTWGTGIHV_light;SRR17729722;IGLV4;PairedNGS|||PRJNA777934|SRR17778139|human|GCTGCAGGTACCTACA|IGHV3_30*04,IGHD4_23*01,IGHJ3*02|IGLV4_69*01,IGLJ1*01,IGLC1|AKVEGGNYVGAFDV|QTWGTGIHV_light;SRR17778139;IGLV4;PairedNGS"
- },
- "heavyChain": {
- "headers": [
- {
- "id": "368.22.A.0062",
- "vGeneSegment": "IGHV3",
- "source": "CoV-AbDab",
- "header": "368.22.A.0062_B-cells SARS-CoV2 Human Patient_human_heavy_"
- },
- {
- "id": "SRR17729722",
- "vGeneSegment": "IGHV3",
- "source": "PairedNGS",
- "header": "PRJNA777934|SRR17729722|human|GCTGCAGGTACCTACA|IGHV3_30*04,IGHD4_23*01,IGHJ3*02,IGHG1|IGLV4_69*01,IGLJ1*01,IGLC1|AKVEGGNYVGAFDV|QTWGTGIHV_heavy"
- },
- {
- "id": "SRR17778139",
- "vGeneSegment": "IGHV3",
- "source": "PairedNGS",
- "header": "PRJNA777934|SRR17778139|human|GCTGCAGGTACCTACA|IGHV3_30*04,IGHD4_23*01,IGHJ3*02|IGLV4_69*01,IGLJ1*01,IGLC1|AKVEGGNYVGAFDV|QTWGTGIHV_heavy"
- }
- ],
- "sequence": "QVQLVESGGGVVQPGRSLRLSCAASGFTFSGYAMHWVRQAPGKGLEWVAVISYDGSNRYYADSVKGRFSISRDNSKKTLYLQMNSLRDEDTAVYYCAKVEGGNYVGAFDVWGQGTMVTVSS",
- "rawFasta": "368.22.A.0062|||368.22.A.0062_B-cells SARS-CoV2 Human Patient_human_heavy_;368.22.A.0062;IGHV3;CoV-AbDab|||PRJNA777934|SRR17729722|human|GCTGCAGGTACCTACA|IGHV3_30*04,IGHD4_23*01,IGHJ3*02,IGHG1|IGLV4_69*01,IGLJ1*01,IGLC1|AKVEGGNYVGAFDV|QTWGTGIHV_heavy;SRR17729722;IGHV3;PairedNGS|||PRJNA777934|SRR17778139|human|GCTGCAGGTACCTACA|IGHV3_30*04,IGHD4_23*01,IGHJ3*02|IGLV4_69*01,IGLJ1*01,IGLC1|AKVEGGNYVGAFDV|QTWGTGIHV_heavy;SRR17778139;IGHV3;PairedNGS"
- }
- }
-
- test('"listSources" should return the list of sources as a Set', () => {
- const sources = Antibody.listSources(antibody)
- const expected = new Set()
- .add('CoV-AbDab')
- .add('PairedNGS')
- expect(sources).toStrictEqual(expected)
- })
-
- test('"listSegments" should return the list of gene segments as an object containg two Sets', () => {
- const segments = Antibody.listSegments(antibody)
- const expected = {
- heavyChain: new Set().add('IGHV3'),
- lightChain: new Set().add('IGLV4')
- }
- expect(segments).toStrictEqual(expected)
- })
-
- test('"generateHashId" should return the SHA256 of the antibody', () => {
- const hashId = Antibody.generateHashId(antibody)
- expect(hashId).toBe(antibody.hashId)
- })
-
- test('"toFasta" should return the FASTA version of the antibody', () => {
- const fasta = Antibody.toFasta(antibody)
- const expected = ">368.22.A.0062|||368.22.A.0062_B-cells SARS-CoV2 Human Patient_human_light_;368.22.A.0062;IGLV4;CoV-AbDab|||PRJNA777934|SRR17729722|human|GCTGCAGGTACCTACA|IGHV3_30*04,IGHD4_23*01,IGHJ3*02,IGHG1|IGLV4_69*01,IGLJ1*01,IGLC1|AKVEGGNYVGAFDV|QTWGTGIHV_light;SRR17729722;IGLV4;PairedNGS|||PRJNA777934|SRR17778139|human|GCTGCAGGTACCTACA|IGHV3_30*04,IGHD4_23*01,IGHJ3*02|IGLV4_69*01,IGLJ1*01,IGLC1|AKVEGGNYVGAFDV|QTWGTGIHV_light;SRR17778139;IGLV4;PairedNGS"
- .concat("\nQLVLTQSPSASASLGASVKLTCTLSSGHSSYAIAWHQQQPEKGPRYLMKLNSDGSHSEGDGIPDRFSGSSSGAERYLTISSLQSEDEADYYCQTWGTGIHVFGTGTKVTVL")
- .concat("\n>368.22.A.0062|||368.22.A.0062_B-cells SARS-CoV2 Human Patient_human_heavy_;368.22.A.0062;IGHV3;CoV-AbDab|||PRJNA777934|SRR17729722|human|GCTGCAGGTACCTACA|IGHV3_30*04,IGHD4_23*01,IGHJ3*02,IGHG1|IGLV4_69*01,IGLJ1*01,IGLC1|AKVEGGNYVGAFDV|QTWGTGIHV_heavy;SRR17729722;IGHV3;PairedNGS|||PRJNA777934|SRR17778139|human|GCTGCAGGTACCTACA|IGHV3_30*04,IGHD4_23*01,IGHJ3*02|IGLV4_69*01,IGLJ1*01,IGLC1|AKVEGGNYVGAFDV|QTWGTGIHV_heavy;SRR17778139;IGHV3;PairedNGS")
- .concat("\nQVQLVESGGGVVQPGRSLRLSCAASGFTFSGYAMHWVRQAPGKGLEWVAVISYDGSNRYYADSVKGRFSISRDNSKKTLYLQMNSLRDEDTAVYYCAKVEGGNYVGAFDVWGQGTMVTVSS")
-
- expect(fasta).toBe(expected)
- })
-
- test('"toString" should return the JSON version of the antibody', () => {
- const json = Antibody.toString(antibody)
- const expected = JSON.stringify(antibody)
-
- expect(json).toBe(expected)
- })
-})
diff --git a/src/server/utils/escapeString.test.js b/src/server/utils/escapeString.test.js
deleted file mode 100644
index f9eb19af3e025dbc6ea198d3ac5f5b893fef6aa0..0000000000000000000000000000000000000000
--- a/src/server/utils/escapeString.test.js
+++ /dev/null
@@ -1,25 +0,0 @@
-// ABSD
-// Copyright (C) 2023 Institut Pasteur
-//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-import { expect, test } from "vitest"
-import escapeString from "./escapeString"
-
-test('Should escape all dangerous characters in a regex', () => {
- const dangerousString = "abc.de*fgh+ijk?lmn^op$qr{st}u(vw)xyzABCDE|FG\HIJK[LM]NOPQRSTUVWXYZ123456789-_%&#@"
- const safeString = "abc\\.de\\*fgh\\+ijk\\?lmn\\^op\\$qr\\{st\\}u\\(vw\\)xyzABCDE\\|FGHIJK\\[LM\\]NOPQRSTUVWXYZ123456789-_%&#@"
-
- expect(escapeString(dangerousString)).toBe(safeString)
-})
diff --git a/vite.config.ts b/vite.config.ts
index f0a8bc86dfa55eeded30af4d2845122fe633e4b2..9bf30c186c309536f93cf82ca23ce74ba23b2385 100644
--- a/vite.config.ts
+++ b/vite.config.ts
@@ -30,11 +30,5 @@ export default defineConfig({
__VUE_OPTIONS_API__: false,
__VUE_PROD_DEVTOOLS__: false,
__VUE_PROD_HYDRATION_MISMATCH_DETAILS__: false
- },
- test: {
- // https://vitest.dev/config/
- name: 'Server tests',
- root: 'src/server',
- include: ['**/*.test.js']
}
})