diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8efadc91cda45cf7e7714b59a042f9a82e9c1028..cd06272d937f09989f48cacde2eb67761be9c214 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -16,25 +16,36 @@ 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
stage: validate
rules:
- changes:
- data/*.fasta
- image: node:22-alpine
script:
- npm run validate
# Build the archive of the fasta files and compute the stats.
# Commit the files in the data folder, triggering another CI.
build-archive-and-stats:
+ image: node:22-alpine
stage: archive
rules:
- if: $CI_COMMIT_BRANCH == "master"
changes:
- data/*.fasta
- image: node:22-alpine
script:
- export CURRENT_DATE=$(date +'%Y-%m-%d')
- export ARCHIVE_PATH=data/${CURRENT_DATE}.tar.gz
@@ -54,10 +65,10 @@ build-archive-and-stats:
# Build the docker image and store it the gitlab registery.
build-docker-image:
+ image: docker:24
stage: build
rules:
- if: $CI_COMMIT_BRANCH == "master" || $CI_COMMIT_BRANCH == "dev"
- image: docker:24
interruptible: true
script:
- docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
@@ -68,10 +79,10 @@ build-docker-image:
# Fetch the image of MongoDB from the DockerHub and store it if there is any changes.
# This avoid issues with Docker in case of overpulling.
fetch-mongo-image:
+ image: docker:24
stage: build
rules:
- if: $CI_COMMIT_BRANCH == "master" || $CI_COMMIT_BRANCH == "dev"
- image: docker:24
interruptible: true
script:
- docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
@@ -81,8 +92,8 @@ fetch-mongo-image:
# Base stage for deploy-dev and deploy-prod
.deploy:
- stage: deploy
image: registry-gitlab.pasteur.fr/dsi-tools/docker-images:docker_kubernetes_image
+ stage: deploy
interruptible: true
script:
- kubectl delete secret registry-gitlab -n ${NAMESPACE} --ignore-not-found=true
diff --git a/package-lock.json b/package-lock.json
index d34f7fd74896711b37ea3b54987946af47961782..7b789b2a249c7ec5d60c55fd54a3c6c43281fa32 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -16,7 +16,7 @@
"fastify": "^5.2.1",
"modern-normalize": "^3.0.1",
"mongodb": "^6.13.0",
- "pinia": "^2.3.1",
+ "pinia": "^3.0.1",
"plotly.js-dist-min": "^3.0.0",
"qs": "^6.14.0",
"vue": "^3.5.13",
@@ -24,7 +24,7 @@
},
"devDependencies": {
"@biomejs/biome": "^1.9.4",
- "@types/node": "^22.13.0",
+ "@types/node": "^22.13.4",
"@types/plotly.js-dist-min": "^2.3.4",
"@types/qs": "^6.9.18",
"@vitejs/plugin-vue": "^5.2.1",
@@ -36,7 +36,8 @@
"rollup-plugin-brotli": "^3.1.0",
"rollup-plugin-gzip": "^4.0.1",
"typescript": "^5.7.3",
- "vite": "^6.0.11",
+ "vite": "^6.1.0",
+ "vitest": "^3.0.5",
"vue-tsc": "^2.2.0"
}
},
@@ -910,9 +911,9 @@
}
},
"node_modules/@rollup/rollup-android-arm-eabi": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-android-arm-eabi/-/rollup-android-arm-eabi-4.28.1.tgz",
- "integrity": "sha512-2aZp8AES04KI2dy3Ss6/MDjXbwBzj+i0GqKtWXgw2/Ma6E4jJvujryO6gJAghIRVz7Vwr9Gtl/8na3nDUKpraQ==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-android-arm-eabi/-/rollup-android-arm-eabi-4.34.6.tgz",
+ "integrity": "sha512-+GcCXtOQoWuC7hhX1P00LqjjIiS/iOouHXhMdiDSnq/1DGTox4SpUvO52Xm+div6+106r+TcvOeo/cxvyEyTgg==",
"cpu": [
"arm"
],
@@ -924,9 +925,9 @@
]
},
"node_modules/@rollup/rollup-android-arm64": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-android-arm64/-/rollup-android-arm64-4.28.1.tgz",
- "integrity": "sha512-EbkK285O+1YMrg57xVA+Dp0tDBRB93/BZKph9XhMjezf6F4TpYjaUSuPt5J0fZXlSag0LmZAsTmdGGqPp4pQFA==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-android-arm64/-/rollup-android-arm64-4.34.6.tgz",
+ "integrity": "sha512-E8+2qCIjciYUnCa1AiVF1BkRgqIGW9KzJeesQqVfyRITGQN+dFuoivO0hnro1DjT74wXLRZ7QF8MIbz+luGaJA==",
"cpu": [
"arm64"
],
@@ -938,9 +939,9 @@
]
},
"node_modules/@rollup/rollup-darwin-arm64": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-darwin-arm64/-/rollup-darwin-arm64-4.28.1.tgz",
- "integrity": "sha512-prduvrMKU6NzMq6nxzQw445zXgaDBbMQvmKSJaxpaZ5R1QDM8w+eGxo6Y/jhT/cLoCvnZI42oEqf9KQNYz1fqQ==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-darwin-arm64/-/rollup-darwin-arm64-4.34.6.tgz",
+ "integrity": "sha512-z9Ib+OzqN3DZEjX7PDQMHEhtF+t6Mi2z/ueChQPLS/qUMKY7Ybn5A2ggFoKRNRh1q1T03YTQfBTQCJZiepESAg==",
"cpu": [
"arm64"
],
@@ -952,9 +953,9 @@
]
},
"node_modules/@rollup/rollup-darwin-x64": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-darwin-x64/-/rollup-darwin-x64-4.28.1.tgz",
- "integrity": "sha512-WsvbOunsUk0wccO/TV4o7IKgloJ942hVFK1CLatwv6TJspcCZb9umQkPdvB7FihmdxgaKR5JyxDjWpCOp4uZlQ==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-darwin-x64/-/rollup-darwin-x64-4.34.6.tgz",
+ "integrity": "sha512-PShKVY4u0FDAR7jskyFIYVyHEPCPnIQY8s5OcXkdU8mz3Y7eXDJPdyM/ZWjkYdR2m0izD9HHWA8sGcXn+Qrsyg==",
"cpu": [
"x64"
],
@@ -966,9 +967,9 @@
]
},
"node_modules/@rollup/rollup-freebsd-arm64": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-freebsd-arm64/-/rollup-freebsd-arm64-4.28.1.tgz",
- "integrity": "sha512-HTDPdY1caUcU4qK23FeeGxCdJF64cKkqajU0iBnTVxS8F7H/7BewvYoG+va1KPSL63kQ1PGNyiwKOfReavzvNA==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-freebsd-arm64/-/rollup-freebsd-arm64-4.34.6.tgz",
+ "integrity": "sha512-YSwyOqlDAdKqs0iKuqvRHLN4SrD2TiswfoLfvYXseKbL47ht1grQpq46MSiQAx6rQEN8o8URtpXARCpqabqxGQ==",
"cpu": [
"arm64"
],
@@ -980,9 +981,9 @@
]
},
"node_modules/@rollup/rollup-freebsd-x64": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-freebsd-x64/-/rollup-freebsd-x64-4.28.1.tgz",
- "integrity": "sha512-m/uYasxkUevcFTeRSM9TeLyPe2QDuqtjkeoTpP9SW0XxUWfcYrGDMkO/m2tTw+4NMAF9P2fU3Mw4ahNvo7QmsQ==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-freebsd-x64/-/rollup-freebsd-x64-4.34.6.tgz",
+ "integrity": "sha512-HEP4CgPAY1RxXwwL5sPFv6BBM3tVeLnshF03HMhJYCNc6kvSqBgTMmsEjb72RkZBAWIqiPUyF1JpEBv5XT9wKQ==",
"cpu": [
"x64"
],
@@ -994,9 +995,9 @@
]
},
"node_modules/@rollup/rollup-linux-arm-gnueabihf": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm-gnueabihf/-/rollup-linux-arm-gnueabihf-4.28.1.tgz",
- "integrity": "sha512-QAg11ZIt6mcmzpNE6JZBpKfJaKkqTm1A9+y9O+frdZJEuhQxiugM05gnCWiANHj4RmbgeVJpTdmKRmH/a+0QbA==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm-gnueabihf/-/rollup-linux-arm-gnueabihf-4.34.6.tgz",
+ "integrity": "sha512-88fSzjC5xeH9S2Vg3rPgXJULkHcLYMkh8faix8DX4h4TIAL65ekwuQMA/g2CXq8W+NJC43V6fUpYZNjaX3+IIg==",
"cpu": [
"arm"
],
@@ -1008,9 +1009,9 @@
]
},
"node_modules/@rollup/rollup-linux-arm-musleabihf": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm-musleabihf/-/rollup-linux-arm-musleabihf-4.28.1.tgz",
- "integrity": "sha512-dRP9PEBfolq1dmMcFqbEPSd9VlRuVWEGSmbxVEfiq2cs2jlZAl0YNxFzAQS2OrQmsLBLAATDMb3Z6MFv5vOcXg==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm-musleabihf/-/rollup-linux-arm-musleabihf-4.34.6.tgz",
+ "integrity": "sha512-wM4ztnutBqYFyvNeR7Av+reWI/enK9tDOTKNF+6Kk2Q96k9bwhDDOlnCUNRPvromlVXo04riSliMBs/Z7RteEg==",
"cpu": [
"arm"
],
@@ -1022,9 +1023,9 @@
]
},
"node_modules/@rollup/rollup-linux-arm64-gnu": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm64-gnu/-/rollup-linux-arm64-gnu-4.28.1.tgz",
- "integrity": "sha512-uGr8khxO+CKT4XU8ZUH1TTEUtlktK6Kgtv0+6bIFSeiSlnGJHG1tSFSjm41uQ9sAO/5ULx9mWOz70jYLyv1QkA==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm64-gnu/-/rollup-linux-arm64-gnu-4.34.6.tgz",
+ "integrity": "sha512-9RyprECbRa9zEjXLtvvshhw4CMrRa3K+0wcp3KME0zmBe1ILmvcVHnypZ/aIDXpRyfhSYSuN4EPdCCj5Du8FIA==",
"cpu": [
"arm64"
],
@@ -1036,9 +1037,9 @@
]
},
"node_modules/@rollup/rollup-linux-arm64-musl": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm64-musl/-/rollup-linux-arm64-musl-4.28.1.tgz",
- "integrity": "sha512-QF54q8MYGAqMLrX2t7tNpi01nvq5RI59UBNx+3+37zoKX5KViPo/gk2QLhsuqok05sSCRluj0D00LzCwBikb0A==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-arm64-musl/-/rollup-linux-arm64-musl-4.34.6.tgz",
+ "integrity": "sha512-qTmklhCTyaJSB05S+iSovfo++EwnIEZxHkzv5dep4qoszUMX5Ca4WM4zAVUMbfdviLgCSQOu5oU8YoGk1s6M9Q==",
"cpu": [
"arm64"
],
@@ -1050,9 +1051,9 @@
]
},
"node_modules/@rollup/rollup-linux-loongarch64-gnu": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-loongarch64-gnu/-/rollup-linux-loongarch64-gnu-4.28.1.tgz",
- "integrity": "sha512-vPul4uodvWvLhRco2w0GcyZcdyBfpfDRgNKU+p35AWEbJ/HPs1tOUrkSueVbBS0RQHAf/A+nNtDpvw95PeVKOA==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-loongarch64-gnu/-/rollup-linux-loongarch64-gnu-4.34.6.tgz",
+ "integrity": "sha512-4Qmkaps9yqmpjY5pvpkfOerYgKNUGzQpFxV6rnS7c/JfYbDSU0y6WpbbredB5cCpLFGJEqYX40WUmxMkwhWCjw==",
"cpu": [
"loong64"
],
@@ -1064,9 +1065,9 @@
]
},
"node_modules/@rollup/rollup-linux-powerpc64le-gnu": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-powerpc64le-gnu/-/rollup-linux-powerpc64le-gnu-4.28.1.tgz",
- "integrity": "sha512-pTnTdBuC2+pt1Rmm2SV7JWRqzhYpEILML4PKODqLz+C7Ou2apEV52h19CR7es+u04KlqplggmN9sqZlekg3R1A==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-powerpc64le-gnu/-/rollup-linux-powerpc64le-gnu-4.34.6.tgz",
+ "integrity": "sha512-Zsrtux3PuaxuBTX/zHdLaFmcofWGzaWW1scwLU3ZbW/X+hSsFbz9wDIp6XvnT7pzYRl9MezWqEqKy7ssmDEnuQ==",
"cpu": [
"ppc64"
],
@@ -1078,9 +1079,9 @@
]
},
"node_modules/@rollup/rollup-linux-riscv64-gnu": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-riscv64-gnu/-/rollup-linux-riscv64-gnu-4.28.1.tgz",
- "integrity": "sha512-vWXy1Nfg7TPBSuAncfInmAI/WZDd5vOklyLJDdIRKABcZWojNDY0NJwruY2AcnCLnRJKSaBgf/GiJfauu8cQZA==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-riscv64-gnu/-/rollup-linux-riscv64-gnu-4.34.6.tgz",
+ "integrity": "sha512-aK+Zp+CRM55iPrlyKiU3/zyhgzWBxLVrw2mwiQSYJRobCURb781+XstzvA8Gkjg/hbdQFuDw44aUOxVQFycrAg==",
"cpu": [
"riscv64"
],
@@ -1092,9 +1093,9 @@
]
},
"node_modules/@rollup/rollup-linux-s390x-gnu": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-s390x-gnu/-/rollup-linux-s390x-gnu-4.28.1.tgz",
- "integrity": "sha512-/yqC2Y53oZjb0yz8PVuGOQQNOTwxcizudunl/tFs1aLvObTclTwZ0JhXF2XcPT/zuaymemCDSuuUPXJJyqeDOg==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-s390x-gnu/-/rollup-linux-s390x-gnu-4.34.6.tgz",
+ "integrity": "sha512-WoKLVrY9ogmaYPXwTH326+ErlCIgMmsoRSx6bO+l68YgJnlOXhygDYSZe/qbUJCSiCiZAQ+tKm88NcWuUXqOzw==",
"cpu": [
"s390x"
],
@@ -1106,9 +1107,9 @@
]
},
"node_modules/@rollup/rollup-linux-x64-gnu": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-x64-gnu/-/rollup-linux-x64-gnu-4.28.1.tgz",
- "integrity": "sha512-fzgeABz7rrAlKYB0y2kSEiURrI0691CSL0+KXwKwhxvj92VULEDQLpBYLHpF49MSiPG4sq5CK3qHMnb9tlCjBw==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-x64-gnu/-/rollup-linux-x64-gnu-4.34.6.tgz",
+ "integrity": "sha512-Sht4aFvmA4ToHd2vFzwMFaQCiYm2lDFho5rPcvPBT5pCdC+GwHG6CMch4GQfmWTQ1SwRKS0dhDYb54khSrjDWw==",
"cpu": [
"x64"
],
@@ -1120,9 +1121,9 @@
]
},
"node_modules/@rollup/rollup-linux-x64-musl": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-x64-musl/-/rollup-linux-x64-musl-4.28.1.tgz",
- "integrity": "sha512-xQTDVzSGiMlSshpJCtudbWyRfLaNiVPXt1WgdWTwWz9n0U12cI2ZVtWe/Jgwyv/6wjL7b66uu61Vg0POWVfz4g==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-linux-x64-musl/-/rollup-linux-x64-musl-4.34.6.tgz",
+ "integrity": "sha512-zmmpOQh8vXc2QITsnCiODCDGXFC8LMi64+/oPpPx5qz3pqv0s6x46ps4xoycfUiVZps5PFn1gksZzo4RGTKT+A==",
"cpu": [
"x64"
],
@@ -1134,9 +1135,9 @@
]
},
"node_modules/@rollup/rollup-win32-arm64-msvc": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-win32-arm64-msvc/-/rollup-win32-arm64-msvc-4.28.1.tgz",
- "integrity": "sha512-wSXmDRVupJstFP7elGMgv+2HqXelQhuNf+IS4V+nUpNVi/GUiBgDmfwD0UGN3pcAnWsgKG3I52wMOBnk1VHr/A==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-win32-arm64-msvc/-/rollup-win32-arm64-msvc-4.34.6.tgz",
+ "integrity": "sha512-3/q1qUsO/tLqGBaD4uXsB6coVGB3usxw3qyeVb59aArCgedSF66MPdgRStUd7vbZOsko/CgVaY5fo2vkvPLWiA==",
"cpu": [
"arm64"
],
@@ -1148,9 +1149,9 @@
]
},
"node_modules/@rollup/rollup-win32-ia32-msvc": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-win32-ia32-msvc/-/rollup-win32-ia32-msvc-4.28.1.tgz",
- "integrity": "sha512-ZkyTJ/9vkgrE/Rk9vhMXhf8l9D+eAhbAVbsGsXKy2ohmJaWg0LPQLnIxRdRp/bKyr8tXuPlXhIoGlEB5XpJnGA==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-win32-ia32-msvc/-/rollup-win32-ia32-msvc-4.34.6.tgz",
+ "integrity": "sha512-oLHxuyywc6efdKVTxvc0135zPrRdtYVjtVD5GUm55I3ODxhU/PwkQFD97z16Xzxa1Fz0AEe4W/2hzRtd+IfpOA==",
"cpu": [
"ia32"
],
@@ -1162,9 +1163,9 @@
]
},
"node_modules/@rollup/rollup-win32-x64-msvc": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/@rollup/rollup-win32-x64-msvc/-/rollup-win32-x64-msvc-4.28.1.tgz",
- "integrity": "sha512-ZvK2jBafvttJjoIdKm/Q/Bh7IJ1Ose9IBOwpOXcOvW3ikGTQGmKDgxTC6oCAzW6PynbkKP8+um1du81XJHZ0JA==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/@rollup/rollup-win32-x64-msvc/-/rollup-win32-x64-msvc-4.34.6.tgz",
+ "integrity": "sha512-0PVwmgzZ8+TZ9oGBmdZoQVXflbvuwzN/HRclujpl4N/q3i+y0lqLw8n1bXA8ru3sApDjlmONaNAuYr38y1Kr9w==",
"cpu": [
"x64"
],
@@ -1192,9 +1193,9 @@
"license": "MIT"
},
"node_modules/@types/node": {
- "version": "22.13.0",
- "resolved": "https://registry.npmjs.org/@types/node/-/node-22.13.0.tgz",
- "integrity": "sha512-ClIbNe36lawluuvq3+YYhnIN2CELi+6q8NpnM7PYp4hBn/TatfboPgVSm2rwKRfnV2M+Ty9GWDFI64KEe+kysA==",
+ "version": "22.13.4",
+ "resolved": "https://registry.npmjs.org/@types/node/-/node-22.13.4.tgz",
+ "integrity": "sha512-ywP2X0DYtX3y08eFVx5fNIw7/uIv8hYUKgXoK8oayJlLnKcRfEYCxWMVE1XagUdVtCJlZT1AU4LXEABW+L1Peg==",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -1252,6 +1253,129 @@
"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"
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+ "version": "3.0.1",
+ "resolved": "https://registry.npmjs.org/pinia/-/pinia-3.0.1.tgz",
+ "integrity": "sha512-WXglsDzztOTH6IfcJ99ltYZin2mY8XZCXujkYWVIJlBjqsP6ST7zw+Aarh63E1cDVYeyUcPCxPHzJpEOmzB6Wg==",
"license": "MIT",
"dependencies": {
- "@vue/devtools-api": "^6.6.3",
- "vue-demi": "^0.14.10"
+ "@vue/devtools-api": "^7.7.2"
},
"funding": {
"url": "https://github.com/sponsors/posva"
@@ -3466,29 +3768,13 @@
}
}
},
- "node_modules/pinia/node_modules/vue-demi": {
- "version": "0.14.10",
- "resolved": "https://registry.npmjs.org/vue-demi/-/vue-demi-0.14.10.tgz",
- "integrity": "sha512-nMZBOwuzabUO0nLgIcc6rycZEebF6eeUfaiQx9+WSk8e29IbLvPU9feI6tqW4kTo3hvoYAJkMh8n8D0fuISphg==",
- "hasInstallScript": true,
- "bin": {
- "vue-demi-fix": "bin/vue-demi-fix.js",
- "vue-demi-switch": "bin/vue-demi-switch.js"
- },
- "engines": {
- "node": ">=12"
- },
- "funding": {
- "url": "https://github.com/sponsors/antfu"
- },
- "peerDependencies": {
- "@vue/composition-api": "^1.0.0-rc.1",
- "vue": "^3.0.0-0 || ^2.6.0"
- },
- "peerDependenciesMeta": {
- "@vue/composition-api": {
- "optional": true
- }
+ "node_modules/pinia/node_modules/@vue/devtools-api": {
+ "version": "7.7.2",
+ "resolved": "https://registry.npmjs.org/@vue/devtools-api/-/devtools-api-7.7.2.tgz",
+ "integrity": "sha512-1syn558KhyN+chO5SjlZIwJ8bV/bQ1nOVTG66t2RbG66ZGekyiYNmRO7X9BJCXQqPsFHlnksqvPhce2qpzxFnA==",
+ "license": "MIT",
+ "dependencies": {
+ "@vue/devtools-kit": "^7.7.2"
}
},
"node_modules/pino": {
@@ -3573,9 +3859,9 @@
"license": "MIT"
},
"node_modules/postcss": {
- "version": "8.4.49",
- "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.49.tgz",
- "integrity": "sha512-OCVPnIObs4N29kxTjzLfUryOkvZEq+pf8jTF0lg8E7uETuWHA+v7j3c/xJmiqpX450191LlmZfUKkXxkTry7nA==",
+ "version": "8.5.2",
+ "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.5.2.tgz",
+ "integrity": "sha512-MjOadfU3Ys9KYoX0AdkBlFEF1Vx37uCCeN4ZHnmwm9FfpbsGWMZeBLMmmpY+6Ocqod7mkdZ0DT31OlbsFrLlkA==",
"funding": [
{
"type": "opencollective",
@@ -3592,7 +3878,7 @@
],
"license": "MIT",
"dependencies": {
- "nanoid": "^3.3.7",
+ "nanoid": "^3.3.8",
"picocolors": "^1.1.1",
"source-map-js": "^1.2.1"
},
@@ -4170,9 +4456,9 @@
"license": "MIT"
},
"node_modules/rollup": {
- "version": "4.28.1",
- "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.28.1.tgz",
- "integrity": "sha512-61fXYl/qNVinKmGSTHAZ6Yy8I3YIJC/r2m9feHo6SwVAVcLT5MPwOUFe7EuURA/4m0NR8lXG4BBXuo/IZEsjMg==",
+ "version": "4.34.6",
+ "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.34.6.tgz",
+ "integrity": "sha512-wc2cBWqJgkU3Iz5oztRkQbfVkbxoz5EhnCGOrnJvnLnQ7O0WhQUYyv18qQI79O8L7DdHrrlJNeCHd4VGpnaXKQ==",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -4186,25 +4472,25 @@
"npm": ">=8.0.0"
},
"optionalDependencies": {
- "@rollup/rollup-android-arm-eabi": "4.28.1",
- "@rollup/rollup-android-arm64": "4.28.1",
- "@rollup/rollup-darwin-arm64": "4.28.1",
- "@rollup/rollup-darwin-x64": "4.28.1",
- "@rollup/rollup-freebsd-arm64": "4.28.1",
- "@rollup/rollup-freebsd-x64": "4.28.1",
- "@rollup/rollup-linux-arm-gnueabihf": "4.28.1",
- "@rollup/rollup-linux-arm-musleabihf": "4.28.1",
- "@rollup/rollup-linux-arm64-gnu": "4.28.1",
- "@rollup/rollup-linux-arm64-musl": "4.28.1",
- "@rollup/rollup-linux-loongarch64-gnu": "4.28.1",
- "@rollup/rollup-linux-powerpc64le-gnu": "4.28.1",
- "@rollup/rollup-linux-riscv64-gnu": "4.28.1",
- "@rollup/rollup-linux-s390x-gnu": "4.28.1",
- "@rollup/rollup-linux-x64-gnu": "4.28.1",
- "@rollup/rollup-linux-x64-musl": "4.28.1",
- "@rollup/rollup-win32-arm64-msvc": "4.28.1",
- "@rollup/rollup-win32-ia32-msvc": "4.28.1",
- "@rollup/rollup-win32-x64-msvc": "4.28.1",
+ "@rollup/rollup-android-arm-eabi": "4.34.6",
+ "@rollup/rollup-android-arm64": "4.34.6",
+ "@rollup/rollup-darwin-arm64": "4.34.6",
+ "@rollup/rollup-darwin-x64": "4.34.6",
+ "@rollup/rollup-freebsd-arm64": "4.34.6",
+ "@rollup/rollup-freebsd-x64": "4.34.6",
+ "@rollup/rollup-linux-arm-gnueabihf": "4.34.6",
+ "@rollup/rollup-linux-arm-musleabihf": "4.34.6",
+ "@rollup/rollup-linux-arm64-gnu": "4.34.6",
+ "@rollup/rollup-linux-arm64-musl": "4.34.6",
+ "@rollup/rollup-linux-loongarch64-gnu": "4.34.6",
+ "@rollup/rollup-linux-powerpc64le-gnu": "4.34.6",
+ "@rollup/rollup-linux-riscv64-gnu": "4.34.6",
+ "@rollup/rollup-linux-s390x-gnu": "4.34.6",
+ "@rollup/rollup-linux-x64-gnu": "4.34.6",
+ "@rollup/rollup-linux-x64-musl": "4.34.6",
+ "@rollup/rollup-win32-arm64-msvc": "4.34.6",
+ "@rollup/rollup-win32-ia32-msvc": "4.34.6",
+ "@rollup/rollup-win32-x64-msvc": "4.34.6",
"fsevents": "~2.3.2"
}
},
@@ -4403,6 +4689,13 @@
"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",
@@ -4453,6 +4746,15 @@
"memory-pager": "^1.0.2"
}
},
+ "node_modules/speakingurl": {
+ "version": "14.0.1",
+ "resolved": "https://registry.npmjs.org/speakingurl/-/speakingurl-14.0.1.tgz",
+ "integrity": "sha512-1POYv7uv2gXoyGFpBCmpDVSNV74IfsWlDW216UPjbWufNf+bSU6GdbDsxdcxtfwb4xlI3yxzOTKClUosxARYrQ==",
+ "license": "BSD-3-Clause",
+ "engines": {
+ "node": ">=0.10.0"
+ }
+ },
"node_modules/split2": {
"version": "4.2.0",
"resolved": "https://registry.npmjs.org/split2/-/split2-4.2.0.tgz",
@@ -4461,6 +4763,13 @@
"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",
@@ -4470,6 +4779,13 @@
"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",
@@ -4558,6 +4874,18 @@
"postcss": "^8.4.31"
}
},
+ "node_modules/superjson": {
+ "version": "2.2.2",
+ "resolved": "https://registry.npmjs.org/superjson/-/superjson-2.2.2.tgz",
+ "integrity": "sha512-5JRxVqC8I8NuOUjzBbvVJAKNM8qoVuH0O77h4WInc/qC2q5IreqKxYwgkga3PfA22OayK2ikceb/B26dztPl+Q==",
+ "license": "MIT",
+ "dependencies": {
+ "copy-anything": "^3.0.2"
+ },
+ "engines": {
+ "node": ">=16"
+ }
+ },
"node_modules/supports-color": {
"version": "8.1.1",
"resolved": "https://registry.npmjs.org/supports-color/-/supports-color-8.1.1.tgz",
@@ -4606,6 +4934,50 @@
"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",
@@ -4746,15 +5118,15 @@
"dev": true
},
"node_modules/vite": {
- "version": "6.0.11",
- "resolved": "https://registry.npmjs.org/vite/-/vite-6.0.11.tgz",
- "integrity": "sha512-4VL9mQPKoHy4+FE0NnRE/kbY51TOfaknxAjt3fJbGJxhIpBZiqVzlZDEesWWsuREXHwNdAoOFZ9MkPEVXczHwg==",
+ "version": "6.1.0",
+ "resolved": "https://registry.npmjs.org/vite/-/vite-6.1.0.tgz",
+ "integrity": "sha512-RjjMipCKVoR4hVfPY6GQTgveinjNuyLw+qruksLDvA5ktI1150VmcMBKmQaEWJhg/j6Uaf6dNCNA0AfdzUb/hQ==",
"dev": true,
"license": "MIT",
"dependencies": {
"esbuild": "^0.24.2",
- "postcss": "^8.4.49",
- "rollup": "^4.23.0"
+ "postcss": "^8.5.1",
+ "rollup": "^4.30.1"
},
"bin": {
"vite": "bin/vite.js"
@@ -4817,6 +5189,99 @@
}
}
},
+ "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",
@@ -4911,6 +5376,23 @@
"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 6dc5c9da13740623bd990a08c9de7be5e13c8363..d2046610b82c220d69bdcdffdea1db0c4eb12498 100644
--- a/package.json
+++ b/package.json
@@ -9,6 +9,7 @@
"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",
@@ -35,7 +36,7 @@
"fastify": "^5.2.1",
"modern-normalize": "^3.0.1",
"mongodb": "^6.13.0",
- "pinia": "^2.3.1",
+ "pinia": "^3.0.1",
"plotly.js-dist-min": "^3.0.0",
"qs": "^6.14.0",
"vue": "^3.5.13",
@@ -43,7 +44,7 @@
},
"devDependencies": {
"@biomejs/biome": "^1.9.4",
- "@types/node": "^22.13.0",
+ "@types/node": "^22.13.4",
"@types/plotly.js-dist-min": "^2.3.4",
"@types/qs": "^6.9.18",
"@vitejs/plugin-vue": "^5.2.1",
@@ -55,7 +56,8 @@
"rollup-plugin-brotli": "^3.1.0",
"rollup-plugin-gzip": "^4.0.1",
"typescript": "^5.7.3",
- "vite": "^6.0.11",
+ "vite": "^6.1.0",
+ "vitest": "^3.0.5",
"vue-tsc": "^2.2.0"
}
}
diff --git a/src/client/store.ts b/src/client/store.ts
index 149d0f742285bbeaa9c091dbc906e416b299eb3b..5d6111d9be0e625db8c7470906e790f82ddeeff4 100644
--- a/src/client/store.ts
+++ b/src/client/store.ts
@@ -102,8 +102,8 @@ export const useStore = defineStore('store', {
countAntibodies(countRequest: APICountParams): void {
// Avoid to send an empty request to get an information
// we already have in the stats.
- if (Object.keys(countRequest).length === 0) {
- this.antibodiesCount = this.statistics?.antibodies || 0
+ if (Object.keys(countRequest).length === 0 && this.statistics?.antibodies) {
+ this.antibodiesCount = this.statistics.antibodies
return
}
diff --git a/src/server/app.js b/src/server/app.js
index a635b5ab67400fc56d785b0c4643c49d5cbc0056..1e0c7913eda6032f357512d87d4d2d9af9f803d2 100644
--- a/src/server/app.js
+++ b/src/server/app.js
@@ -27,7 +27,7 @@ import antibodiesCountRoute from './routes/antibodiesCountRoute.js'
import antibodiesDownloadArchiveFileRoute from './routes/antibodiesDownloadArchiveFileRoute.js'
import antibodiesDownloadArchiveRoute from './routes/antibodiesDownloadArchiveRoute.js'
import antibodiesDownloadRoute from './routes/antibodiesDownloadRoute.js'
-import antibodiesFindOneRoute from './routes/antibodiesFindOneRoute.js'
+import antibodiesFindByIdRoute from './routes/antibodiesFindByIdRoute.js'
import antibodiesFindRoute from './routes/antibodiesFindRoute.js'
import antibodiesSourcesRoute from './routes/antibodiesSourcesRoute.js'
import antibodiesSpeciesRoute from './routes/antibodiesSpeciesRoute.js'
@@ -107,7 +107,7 @@ fastify.route(antibodiesCountRoute)
fastify.route(antibodiesDownloadArchiveFileRoute)
fastify.route(antibodiesDownloadArchiveRoute)
fastify.route(antibodiesDownloadRoute)
-fastify.route(antibodiesFindOneRoute)
+fastify.route(antibodiesFindByIdRoute)
fastify.route(antibodiesFindRoute)
fastify.route(antibodiesSourcesRoute)
fastify.route(antibodiesSpeciesRoute)
diff --git a/src/server/config/env.test.js b/src/server/config/env.test.js
new file mode 100644
index 0000000000000000000000000000000000000000..f026aa22e75fd81a8d0c3614ae0471a1e80adde3
--- /dev/null
+++ b/src/server/config/env.test.js
@@ -0,0 +1,69 @@
+// 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
new file mode 100644
index 0000000000000000000000000000000000000000..7dd24c344dbdc7f03a9a42db11e63f6cf29c4119
--- /dev/null
+++ b/src/server/models/Antibody.test.js
@@ -0,0 +1,140 @@
+// 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/routes/antibodiesFindOneRoute.js b/src/server/routes/antibodiesFindByIdRoute.js
similarity index 92%
rename from src/server/routes/antibodiesFindOneRoute.js
rename to src/server/routes/antibodiesFindByIdRoute.js
index d2a81221736adfad3b013b62c5c2d4288d0634c6..975b81a785b7dff2e00349c5c45f5cab5ed3982f 100644
--- a/src/server/routes/antibodiesFindOneRoute.js
+++ b/src/server/routes/antibodiesFindByIdRoute.js
@@ -23,7 +23,11 @@ export default {
handler: function (request, reply) {
this.mongo.db
.collection('antibodies')
- .findOne({ hashId: request.params.hashId })
+ .findOne({
+ hashId: request.params.hashId
+ }, {
+ projection: { _id: false }
+ })
.then(antibody => {
return reply
.code(200)
diff --git a/src/server/utils/escapeString.js b/src/server/utils/escapeString.js
index 2606aec6d02669af6ed19a6ce3ec5465be10050c..2d06104b1da8fbdfed68b48c3927849737ada7dc 100644
--- a/src/server/utils/escapeString.js
+++ b/src/server/utils/escapeString.js
@@ -15,7 +15,7 @@
// along with this program. If not, see <http://www.gnu.org/licenses/>.
/**
- * Escape all special charcaters in a string to make it safe
+ * Escape all special characters in a string to make it safe
* to use in a regex.
* @link https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_expressions#escaping
* @param {string} string - The string containing characters to escape
diff --git a/src/server/utils/escapeString.test.js b/src/server/utils/escapeString.test.js
new file mode 100644
index 0000000000000000000000000000000000000000..f9eb19af3e025dbc6ea198d3ac5f5b893fef6aa0
--- /dev/null
+++ b/src/server/utils/escapeString.test.js
@@ -0,0 +1,25 @@
+// 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 3bdd5fe50f1706e4186a71709382434ba240f19c..f0a8bc86dfa55eeded30af4d2845122fe633e4b2 100644
--- a/vite.config.ts
+++ b/vite.config.ts
@@ -1,3 +1,4 @@
+/// <reference types='vitest' />
import { defineConfig } from 'vite'
import vue from '@vitejs/plugin-vue'
import brotliPlugin from 'rollup-plugin-brotli'
@@ -29,5 +30,11 @@ 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']
}
})