diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cd06272d937f09989f48cacde2eb67761be9c214..5c21bd91918846ee3c7fbeb8ef6b112aad29d324 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -16,20 +16,9 @@ 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
+ image: node:22-alpine3.21
stage: validate
rules:
- changes:
@@ -40,7 +29,7 @@ validate-fasta-files:
# 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
+ image: node:22-alpine3.21
stage: archive
rules:
- if: $CI_COMMIT_BRANCH == "master"
diff --git a/Dockerfile b/Dockerfile
index 8805e9642b765f9f45cf65ef59ed735739f1d2a9..545aba352769ee4f80bb65572a7777651fa543dc 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,7 +1,7 @@
# Builder image
# =============
-FROM node:22-alpine AS builder
+FROM node:22-alpine3.21 AS builder
WORKDIR /usr/build
# Copy only the relevant files to build the application
@@ -22,7 +22,7 @@ RUN npm run build
# Production image
# ================
-FROM node:22-alpine
+FROM node:22-alpine3.21
WORKDIR /usr/src/absd
ENV NODE_ENV="production"
diff --git a/LICENSE b/LICENSE
index d4dced0f4ea2b57c5f7bda16e91b34c64e1cbf41..5497ce15ea891b55846573a60842e7fe90c12d73 100644
--- a/LICENSE
+++ b/LICENSE
@@ -632,7 +632,7 @@ state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
ABSD
- Copyright (C) 2023 Institut Pasteur
+ Copyright (C) 2025 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
@@ -652,7 +652,7 @@ Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
- <program> Copyright (C) 2023 Institut Pasteur
+ <program> Copyright (C) 2025 Institut Pasteur
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
diff --git a/biome.json b/biome.json
index b724216311f220e92778bda923ac76e7ed274393..fc39e6cad10ac3ddf37e52a2f48bec917eda66f4 100644
--- a/biome.json
+++ b/biome.json
@@ -22,7 +22,8 @@
"recommended": true,
"complexity": {
"noForEach": "off",
- "useArrowFunction": "off"
+ "useArrowFunction": "off",
+ "noStaticOnlyClass": "off"
}
}
}
diff --git a/package-lock.json b/package-lock.json
index 7b789b2a249c7ec5d60c55fd54a3c6c43281fa32..99ee1347ec9f68f7a12da5fe7c5de160c5188afd 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -10,21 +10,21 @@
"license": "GPL-3.0",
"dependencies": {
"@fastify/mongodb": "^9.0.2",
- "@fastify/static": "^8.1.0",
+ "@fastify/static": "^8.1.1",
"axios": "^1.7.9",
"env-schema": "^6.0.1",
"fastify": "^5.2.1",
"modern-normalize": "^3.0.1",
- "mongodb": "^6.13.0",
+ "mongodb": "^6.13.1",
"pinia": "^3.0.1",
- "plotly.js-dist-min": "^3.0.0",
+ "plotly.js-dist-min": "^3.0.1",
"qs": "^6.14.0",
"vue": "^3.5.13",
"vue-router": "^4.5.0"
},
"devDependencies": {
"@biomejs/biome": "^1.9.4",
- "@types/node": "^22.13.4",
+ "@types/node": "^22.13.5",
"@types/plotly.js-dist-min": "^2.3.4",
"@types/qs": "^6.9.18",
"@vitejs/plugin-vue": "^5.2.1",
@@ -36,9 +36,8 @@
"rollup-plugin-brotli": "^3.1.0",
"rollup-plugin-gzip": "^4.0.1",
"typescript": "^5.7.3",
- "vite": "^6.1.0",
- "vitest": "^3.0.5",
- "vue-tsc": "^2.2.0"
+ "vite": "^6.2.0",
+ "vue-tsc": "^2.2.4"
}
},
"node_modules/@babel/helper-string-parser": {
@@ -252,9 +251,9 @@
}
},
"node_modules/@esbuild/aix-ppc64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/aix-ppc64/-/aix-ppc64-0.24.2.tgz",
- "integrity": "sha512-thpVCb/rhxE/BnMLQ7GReQLLN8q9qbHmI55F4489/ByVg2aQaQ6kbcLb6FHkocZzQhxc4gx0sCk0tJkKBFzDhA==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/aix-ppc64/-/aix-ppc64-0.25.0.tgz",
+ "integrity": "sha512-O7vun9Sf8DFjH2UtqK8Ku3LkquL9SZL8OLY1T5NZkA34+wG3OQF7cl4Ql8vdNzM6fzBbYfLaiRLIOZ+2FOCgBQ==",
"cpu": [
"ppc64"
],
@@ -269,9 +268,9 @@
}
},
"node_modules/@esbuild/android-arm": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/android-arm/-/android-arm-0.24.2.tgz",
- "integrity": "sha512-tmwl4hJkCfNHwFB3nBa8z1Uy3ypZpxqxfTQOcHX+xRByyYgunVbZ9MzUUfb0RxaHIMnbHagwAxuTL+tnNM+1/Q==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/android-arm/-/android-arm-0.25.0.tgz",
+ "integrity": "sha512-PTyWCYYiU0+1eJKmw21lWtC+d08JDZPQ5g+kFyxP0V+es6VPPSUhM6zk8iImp2jbV6GwjX4pap0JFbUQN65X1g==",
"cpu": [
"arm"
],
@@ -286,9 +285,9 @@
}
},
"node_modules/@esbuild/android-arm64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/android-arm64/-/android-arm64-0.24.2.tgz",
- "integrity": "sha512-cNLgeqCqV8WxfcTIOeL4OAtSmL8JjcN6m09XIgro1Wi7cF4t/THaWEa7eL5CMoMBdjoHOTh/vwTO/o2TRXIyzg==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/android-arm64/-/android-arm64-0.25.0.tgz",
+ "integrity": "sha512-grvv8WncGjDSyUBjN9yHXNt+cq0snxXbDxy5pJtzMKGmmpPxeAmAhWxXI+01lU5rwZomDgD3kJwulEnhTRUd6g==",
"cpu": [
"arm64"
],
@@ -303,9 +302,9 @@
}
},
"node_modules/@esbuild/android-x64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/android-x64/-/android-x64-0.24.2.tgz",
- "integrity": "sha512-B6Q0YQDqMx9D7rvIcsXfmJfvUYLoP722bgfBlO5cGvNVb5V/+Y7nhBE3mHV9OpxBf4eAS2S68KZztiPaWq4XYw==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/android-x64/-/android-x64-0.25.0.tgz",
+ "integrity": "sha512-m/ix7SfKG5buCnxasr52+LI78SQ+wgdENi9CqyCXwjVR2X4Jkz+BpC3le3AoBPYTC9NHklwngVXvbJ9/Akhrfg==",
"cpu": [
"x64"
],
@@ -320,9 +319,9 @@
}
},
"node_modules/@esbuild/darwin-arm64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/darwin-arm64/-/darwin-arm64-0.24.2.tgz",
- "integrity": "sha512-kj3AnYWc+CekmZnS5IPu9D+HWtUI49hbnyqk0FLEJDbzCIQt7hg7ucF1SQAilhtYpIujfaHr6O0UHlzzSPdOeA==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/darwin-arm64/-/darwin-arm64-0.25.0.tgz",
+ "integrity": "sha512-mVwdUb5SRkPayVadIOI78K7aAnPamoeFR2bT5nszFUZ9P8UpK4ratOdYbZZXYSqPKMHfS1wdHCJk1P1EZpRdvw==",
"cpu": [
"arm64"
],
@@ -337,9 +336,9 @@
}
},
"node_modules/@esbuild/darwin-x64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/darwin-x64/-/darwin-x64-0.24.2.tgz",
- "integrity": "sha512-WeSrmwwHaPkNR5H3yYfowhZcbriGqooyu3zI/3GGpF8AyUdsrrP0X6KumITGA9WOyiJavnGZUwPGvxvwfWPHIA==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/darwin-x64/-/darwin-x64-0.25.0.tgz",
+ "integrity": "sha512-DgDaYsPWFTS4S3nWpFcMn/33ZZwAAeAFKNHNa1QN0rI4pUjgqf0f7ONmXf6d22tqTY+H9FNdgeaAa+YIFUn2Rg==",
"cpu": [
"x64"
],
@@ -354,9 +353,9 @@
}
},
"node_modules/@esbuild/freebsd-arm64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/freebsd-arm64/-/freebsd-arm64-0.24.2.tgz",
- "integrity": "sha512-UN8HXjtJ0k/Mj6a9+5u6+2eZ2ERD7Edt1Q9IZiB5UZAIdPnVKDoG7mdTVGhHJIeEml60JteamR3qhsr1r8gXvg==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/freebsd-arm64/-/freebsd-arm64-0.25.0.tgz",
+ "integrity": "sha512-VN4ocxy6dxefN1MepBx/iD1dH5K8qNtNe227I0mnTRjry8tj5MRk4zprLEdG8WPyAPb93/e4pSgi1SoHdgOa4w==",
"cpu": [
"arm64"
],
@@ -371,9 +370,9 @@
}
},
"node_modules/@esbuild/freebsd-x64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/freebsd-x64/-/freebsd-x64-0.24.2.tgz",
- "integrity": "sha512-TvW7wE/89PYW+IevEJXZ5sF6gJRDY/14hyIGFXdIucxCsbRmLUcjseQu1SyTko+2idmCw94TgyaEZi9HUSOe3Q==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/freebsd-x64/-/freebsd-x64-0.25.0.tgz",
+ "integrity": "sha512-mrSgt7lCh07FY+hDD1TxiTyIHyttn6vnjesnPoVDNmDfOmggTLXRv8Id5fNZey1gl/V2dyVK1VXXqVsQIiAk+A==",
"cpu": [
"x64"
],
@@ -388,9 +387,9 @@
}
},
"node_modules/@esbuild/linux-arm": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-arm/-/linux-arm-0.24.2.tgz",
- "integrity": "sha512-n0WRM/gWIdU29J57hJyUdIsk0WarGd6To0s+Y+LwvlC55wt+GT/OgkwoXCXvIue1i1sSNWblHEig00GBWiJgfA==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-arm/-/linux-arm-0.25.0.tgz",
+ "integrity": "sha512-vkB3IYj2IDo3g9xX7HqhPYxVkNQe8qTK55fraQyTzTX/fxaDtXiEnavv9geOsonh2Fd2RMB+i5cbhu2zMNWJwg==",
"cpu": [
"arm"
],
@@ -405,9 +404,9 @@
}
},
"node_modules/@esbuild/linux-arm64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-arm64/-/linux-arm64-0.24.2.tgz",
- "integrity": "sha512-7HnAD6074BW43YvvUmE/35Id9/NB7BeX5EoNkK9obndmZBUk8xmJJeU7DwmUeN7tkysslb2eSl6CTrYz6oEMQg==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-arm64/-/linux-arm64-0.25.0.tgz",
+ "integrity": "sha512-9QAQjTWNDM/Vk2bgBl17yWuZxZNQIF0OUUuPZRKoDtqF2k4EtYbpyiG5/Dk7nqeK6kIJWPYldkOcBqjXjrUlmg==",
"cpu": [
"arm64"
],
@@ -422,9 +421,9 @@
}
},
"node_modules/@esbuild/linux-ia32": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-ia32/-/linux-ia32-0.24.2.tgz",
- "integrity": "sha512-sfv0tGPQhcZOgTKO3oBE9xpHuUqguHvSo4jl+wjnKwFpapx+vUDcawbwPNuBIAYdRAvIDBfZVvXprIj3HA+Ugw==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-ia32/-/linux-ia32-0.25.0.tgz",
+ "integrity": "sha512-43ET5bHbphBegyeqLb7I1eYn2P/JYGNmzzdidq/w0T8E2SsYL1U6un2NFROFRg1JZLTzdCoRomg8Rvf9M6W6Gg==",
"cpu": [
"ia32"
],
@@ -439,9 +438,9 @@
}
},
"node_modules/@esbuild/linux-loong64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-loong64/-/linux-loong64-0.24.2.tgz",
- "integrity": "sha512-CN9AZr8kEndGooS35ntToZLTQLHEjtVB5n7dl8ZcTZMonJ7CCfStrYhrzF97eAecqVbVJ7APOEe18RPI4KLhwQ==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-loong64/-/linux-loong64-0.25.0.tgz",
+ "integrity": "sha512-fC95c/xyNFueMhClxJmeRIj2yrSMdDfmqJnyOY4ZqsALkDrrKJfIg5NTMSzVBr5YW1jf+l7/cndBfP3MSDpoHw==",
"cpu": [
"loong64"
],
@@ -456,9 +455,9 @@
}
},
"node_modules/@esbuild/linux-mips64el": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-mips64el/-/linux-mips64el-0.24.2.tgz",
- "integrity": "sha512-iMkk7qr/wl3exJATwkISxI7kTcmHKE+BlymIAbHO8xanq/TjHaaVThFF6ipWzPHryoFsesNQJPE/3wFJw4+huw==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-mips64el/-/linux-mips64el-0.25.0.tgz",
+ "integrity": "sha512-nkAMFju7KDW73T1DdH7glcyIptm95a7Le8irTQNO/qtkoyypZAnjchQgooFUDQhNAy4iu08N79W4T4pMBwhPwQ==",
"cpu": [
"mips64el"
],
@@ -473,9 +472,9 @@
}
},
"node_modules/@esbuild/linux-ppc64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-ppc64/-/linux-ppc64-0.24.2.tgz",
- "integrity": "sha512-shsVrgCZ57Vr2L8mm39kO5PPIb+843FStGt7sGGoqiiWYconSxwTiuswC1VJZLCjNiMLAMh34jg4VSEQb+iEbw==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-ppc64/-/linux-ppc64-0.25.0.tgz",
+ "integrity": "sha512-NhyOejdhRGS8Iwv+KKR2zTq2PpysF9XqY+Zk77vQHqNbo/PwZCzB5/h7VGuREZm1fixhs4Q/qWRSi5zmAiO4Fw==",
"cpu": [
"ppc64"
],
@@ -490,9 +489,9 @@
}
},
"node_modules/@esbuild/linux-riscv64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-riscv64/-/linux-riscv64-0.24.2.tgz",
- "integrity": "sha512-4eSFWnU9Hhd68fW16GD0TINewo1L6dRrB+oLNNbYyMUAeOD2yCK5KXGK1GH4qD/kT+bTEXjsyTCiJGHPZ3eM9Q==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-riscv64/-/linux-riscv64-0.25.0.tgz",
+ "integrity": "sha512-5S/rbP5OY+GHLC5qXp1y/Mx//e92L1YDqkiBbO9TQOvuFXM+iDqUNG5XopAnXoRH3FjIUDkeGcY1cgNvnXp/kA==",
"cpu": [
"riscv64"
],
@@ -507,9 +506,9 @@
}
},
"node_modules/@esbuild/linux-s390x": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-s390x/-/linux-s390x-0.24.2.tgz",
- "integrity": "sha512-S0Bh0A53b0YHL2XEXC20bHLuGMOhFDO6GN4b3YjRLK//Ep3ql3erpNcPlEFed93hsQAjAQDNsvcK+hV90FubSw==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-s390x/-/linux-s390x-0.25.0.tgz",
+ "integrity": "sha512-XM2BFsEBz0Fw37V0zU4CXfcfuACMrppsMFKdYY2WuTS3yi8O1nFOhil/xhKTmE1nPmVyvQJjJivgDT+xh8pXJA==",
"cpu": [
"s390x"
],
@@ -524,9 +523,9 @@
}
},
"node_modules/@esbuild/linux-x64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-x64/-/linux-x64-0.24.2.tgz",
- "integrity": "sha512-8Qi4nQcCTbLnK9WoMjdC9NiTG6/E38RNICU6sUNqK0QFxCYgoARqVqxdFmWkdonVsvGqWhmm7MO0jyTqLqwj0Q==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-x64/-/linux-x64-0.25.0.tgz",
+ "integrity": "sha512-9yl91rHw/cpwMCNytUDxwj2XjFpxML0y9HAOH9pNVQDpQrBxHy01Dx+vaMu0N1CKa/RzBD2hB4u//nfc+Sd3Cw==",
"cpu": [
"x64"
],
@@ -541,9 +540,9 @@
}
},
"node_modules/@esbuild/netbsd-arm64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/netbsd-arm64/-/netbsd-arm64-0.24.2.tgz",
- "integrity": "sha512-wuLK/VztRRpMt9zyHSazyCVdCXlpHkKm34WUyinD2lzK07FAHTq0KQvZZlXikNWkDGoT6x3TD51jKQ7gMVpopw==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/netbsd-arm64/-/netbsd-arm64-0.25.0.tgz",
+ "integrity": "sha512-RuG4PSMPFfrkH6UwCAqBzauBWTygTvb1nxWasEJooGSJ/NwRw7b2HOwyRTQIU97Hq37l3npXoZGYMy3b3xYvPw==",
"cpu": [
"arm64"
],
@@ -558,9 +557,9 @@
}
},
"node_modules/@esbuild/netbsd-x64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/netbsd-x64/-/netbsd-x64-0.24.2.tgz",
- "integrity": "sha512-VefFaQUc4FMmJuAxmIHgUmfNiLXY438XrL4GDNV1Y1H/RW3qow68xTwjZKfj/+Plp9NANmzbH5R40Meudu8mmw==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/netbsd-x64/-/netbsd-x64-0.25.0.tgz",
+ "integrity": "sha512-jl+qisSB5jk01N5f7sPCsBENCOlPiS/xptD5yxOx2oqQfyourJwIKLRA2yqWdifj3owQZCL2sn6o08dBzZGQzA==",
"cpu": [
"x64"
],
@@ -575,9 +574,9 @@
}
},
"node_modules/@esbuild/openbsd-arm64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/openbsd-arm64/-/openbsd-arm64-0.24.2.tgz",
- "integrity": "sha512-YQbi46SBct6iKnszhSvdluqDmxCJA+Pu280Av9WICNwQmMxV7nLRHZfjQzwbPs3jeWnuAhE9Jy0NrnJ12Oz+0A==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/openbsd-arm64/-/openbsd-arm64-0.25.0.tgz",
+ "integrity": "sha512-21sUNbq2r84YE+SJDfaQRvdgznTD8Xc0oc3p3iW/a1EVWeNj/SdUCbm5U0itZPQYRuRTW20fPMWMpcrciH2EJw==",
"cpu": [
"arm64"
],
@@ -592,9 +591,9 @@
}
},
"node_modules/@esbuild/openbsd-x64": {
- "version": "0.24.2",
- "resolved": "https://registry.npmjs.org/@esbuild/openbsd-x64/-/openbsd-x64-0.24.2.tgz",
- "integrity": "sha512-+iDS6zpNM6EnJyWv0bMGLWSWeXGN/HTaF/LXHXHwejGsVi+ooqDfMCCTerNFxEkM3wYVcExkeGXNqshc9iMaOA==",
+ "version": "0.25.0",
+ "resolved": "https://registry.npmjs.org/@esbuild/openbsd-x64/-/openbsd-x64-0.25.0.tgz",
+ "integrity": "sha512-2gwwriSMPcCFRlPlKx3zLQhfN/2WjJ2NSlg5TKLQOJdV0mSxIcYNTMhk3H3ulL/cak+Xj0lY1Ym9ysDV1igceg==",
"cpu": [
"x64"
],
@@ -609,9 +608,9 @@
}
},
"node_modules/@esbuild/sunos-x64": {
- "version": "0.24.2",
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@@ -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",
@@ -3453,20 +3248,20 @@
}
},
"node_modules/mongodb": {
- "version": "6.13.0",
- "resolved": "https://registry.npmjs.org/mongodb/-/mongodb-6.13.0.tgz",
- "integrity": "sha512-KeESYR5TEaFxOuwRqkOm3XOsMqCSkdeDMjaW5u2nuKfX7rqaofp7JQGoi7sVqQcNJTKuveNbzZtWMstb8ABP6Q==",
+ "version": "6.13.1",
+ "resolved": "https://registry.npmjs.org/mongodb/-/mongodb-6.13.1.tgz",
+ "integrity": "sha512-gdq40tX8StmhP6akMp1pPoEVv+9jTYFSrga/g23JxajPAQhH39ysZrHGzQCSd9PEOnuEQEdjIWqxO7ZSwC0w7Q==",
"license": "Apache-2.0",
"dependencies": {
"@mongodb-js/saslprep": "^1.1.9",
- "bson": "^6.10.1",
+ "bson": "^6.10.3",
"mongodb-connection-string-url": "^3.0.0"
},
"engines": {
"node": ">=16.20.1"
},
"peerDependencies": {
- "@aws-sdk/credential-providers": "^3.188.0",
+ "@aws-sdk/credential-providers": "^3.632.0",
"@mongodb-js/zstd": "^1.1.0 || ^2.0.0",
"gcp-metadata": "^5.2.0",
"kerberos": "^2.0.1",
@@ -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",
@@ -3853,15 +3631,15 @@
"integrity": "sha512-mqn0kFRl0EoqhnL0GQ0veqFHyIN1yig9RHh/InzORTUiZHFRAur+aMtRkELNwGs9aNwKS6tg/An4NYBPGwvtzQ=="
},
"node_modules/plotly.js-dist-min": {
- "version": "3.0.0",
- "resolved": "https://registry.npmjs.org/plotly.js-dist-min/-/plotly.js-dist-min-3.0.0.tgz",
- "integrity": "sha512-AlU1XkNRzwUI55A+kJYj0xJETp3h7aeFe4O1cmhzOryscYdw9jOywXZo+7Zy+y2kEKq12CnTzII4jV7Vgpy4xQ==",
+ "version": "3.0.1",
+ "resolved": "https://registry.npmjs.org/plotly.js-dist-min/-/plotly.js-dist-min-3.0.1.tgz",
+ "integrity": "sha512-RReOqr6TfoHaTbVAoHR1UbTCOSRDsQ7Hbthd+3XAxOwaKmxCE3oejMhLG7urQSqWC65DAcSKV23kZd8e+7mG7w==",
"license": "MIT"
},
"node_modules/postcss": {
- "version": "8.5.2",
- "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.5.2.tgz",
- "integrity": "sha512-MjOadfU3Ys9KYoX0AdkBlFEF1Vx37uCCeN4ZHnmwm9FfpbsGWMZeBLMmmpY+6Ocqod7mkdZ0DT31OlbsFrLlkA==",
+ "version": "8.5.3",
+ "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.5.3.tgz",
+ "integrity": "sha512-dle9A3yYxlBSrt8Fu+IpjGT8SY8hN0mlaA6GY8t0P5PjIOZemULz/E2Bnm/2dcUOena75OTNkHI76uZBNUUq3A==",
"funding": [
{
"type": "opencollective",
@@ -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",
@@ -5118,14 +4831,14 @@
"dev": true
},
"node_modules/vite": {
- "version": "6.1.0",
- "resolved": "https://registry.npmjs.org/vite/-/vite-6.1.0.tgz",
- "integrity": "sha512-RjjMipCKVoR4hVfPY6GQTgveinjNuyLw+qruksLDvA5ktI1150VmcMBKmQaEWJhg/j6Uaf6dNCNA0AfdzUb/hQ==",
+ "version": "6.2.0",
+ "resolved": "https://registry.npmjs.org/vite/-/vite-6.2.0.tgz",
+ "integrity": "sha512-7dPxoo+WsT/64rDcwoOjk76XHj+TqNTIvHKcuMQ1k4/SeHDaQt5GFAeLYzrimZrMpn/O6DtdI03WUjdxuPM0oQ==",
"dev": true,
"license": "MIT",
"dependencies": {
- "esbuild": "^0.24.2",
- "postcss": "^8.5.1",
+ "esbuild": "^0.25.0",
+ "postcss": "^8.5.3",
"rollup": "^4.30.1"
},
"bin": {
@@ -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",
@@ -5326,14 +4946,14 @@
}
},
"node_modules/vue-tsc": {
- "version": "2.2.0",
- "resolved": "https://registry.npmjs.org/vue-tsc/-/vue-tsc-2.2.0.tgz",
- "integrity": "sha512-gtmM1sUuJ8aSb0KoAFmK9yMxb8TxjewmxqTJ1aKphD5Cbu0rULFY6+UQT51zW7SpUcenfPUuflKyVwyx9Qdnxg==",
+ "version": "2.2.4",
+ "resolved": "https://registry.npmjs.org/vue-tsc/-/vue-tsc-2.2.4.tgz",
+ "integrity": "sha512-3EVHlxtpMXcb5bCaK7QDFTbEkMusDfVk0HVRrkv5hEb+Clpu9a96lKUXJAeD/akRlkoA4H8MCHgBDN19S6FnzA==",
"dev": true,
"license": "MIT",
"dependencies": {
"@volar/typescript": "~2.4.11",
- "@vue/language-core": "2.2.0"
+ "@vue/language-core": "2.2.4"
},
"bin": {
"vue-tsc": "bin/vue-tsc.js"
@@ -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..90e611ead3818a659465ca521b4448ef6cb0e3a9 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",
@@ -30,21 +29,21 @@
"license": "GPL-3.0",
"dependencies": {
"@fastify/mongodb": "^9.0.2",
- "@fastify/static": "^8.1.0",
+ "@fastify/static": "^8.1.1",
"axios": "^1.7.9",
"env-schema": "^6.0.1",
"fastify": "^5.2.1",
"modern-normalize": "^3.0.1",
- "mongodb": "^6.13.0",
+ "mongodb": "^6.13.1",
"pinia": "^3.0.1",
- "plotly.js-dist-min": "^3.0.0",
+ "plotly.js-dist-min": "^3.0.1",
"qs": "^6.14.0",
"vue": "^3.5.13",
"vue-router": "^4.5.0"
},
"devDependencies": {
"@biomejs/biome": "^1.9.4",
- "@types/node": "^22.13.4",
+ "@types/node": "^22.13.5",
"@types/plotly.js-dist-min": "^2.3.4",
"@types/qs": "^6.9.18",
"@vitejs/plugin-vue": "^5.2.1",
@@ -56,8 +55,7 @@
"rollup-plugin-brotli": "^3.1.0",
"rollup-plugin-gzip": "^4.0.1",
"typescript": "^5.7.3",
- "vite": "^6.1.0",
- "vitest": "^3.0.5",
- "vue-tsc": "^2.2.0"
+ "vite": "^6.2.0",
+ "vue-tsc": "^2.2.4"
}
}
diff --git a/src/client/api.ts b/src/client/api.ts
index ca2db43e8496af498b7901b333ec183c2f757987..666d89893cf47ac7060361c0a8ee1c7e355297c3 100644
--- a/src/client/api.ts
+++ b/src/client/api.ts
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 axios, { type AxiosResponse } from 'axios'
import qs from 'qs'
import type {
diff --git a/src/client/components/AntibodiesTable.vue b/src/client/components/AntibodiesTable.vue
index 2d02d4fcf853cc952f4220c79486699365b22231..7b0ebfaac6453b83da0366796786947e3e68e5e9 100644
--- a/src/client/components/AntibodiesTable.vue
+++ b/src/client/components/AntibodiesTable.vue
@@ -1,5 +1,5 @@
<template>
- <section class="data-table">
+ <section class="data-table" :aria-busy="isFetchingAntibodies">
<div class="table-header">
<AntibodiesTableTotal />
<AntibodiesTableDownload />
@@ -79,7 +79,7 @@
data-label="ID"
class="link-cell"
>
- <span class="loader" v-if="isFetchingAntibodies"></span>
+ <span class="loader" v-if="isFetchingAntibodies" role="progressbar"></span>
<RouterLink v-else :to="{ name: 'AntibodyPage', params: { hashId: antibody.hashId } }">
{{ antibody.id }}
</RouterLink>
@@ -88,28 +88,28 @@
headers="antibodies-species"
data-label="SPECIES"
>
- <span class="loader" v-if="isFetchingAntibodies"></span>
+ <span class="loader" v-if="isFetchingAntibodies" role="progressbar"></span>
<i v-else>{{ antibody.species }}</i>
</td>
<td
headers="antibodies-heavy-chain"
data-label="HEAVY CHAIN"
>
- <span class="loader" v-if="isFetchingAntibodies"></span>
+ <span class="loader" v-if="isFetchingAntibodies" role="progressbar"></span>
<span v-else>{{ antibody.heavyChain.sequence.substring(0, 15) }}...</span>
</td>
<td
headers="antibodies-light-chain"
data-label="LIGHT CHAIN"
>
- <span class="loader" v-if="isFetchingAntibodies"></span>
+ <span class="loader" v-if="isFetchingAntibodies" role="progressbar"></span>
<span v-else>{{ antibody.lightChain.sequence.substring(0, 15) }}...</span>
</td>
<td
headers="antibodies-sources"
data-label="SOURCES"
>
- <span class="loader" v-if="isFetchingAntibodies"></span>
+ <span class="loader" v-if="isFetchingAntibodies" role="progressbar"></span>
<span v-else>{{ listSources(antibody).join(', ') }}</span>
</td>
</tr>
@@ -207,6 +207,10 @@ function listSources(antibody: Antibody): string[] {
white-space: nowrap;
}
+span[role=progressbar] {
+ vertical-align: middle;
+}
+
@media screen and (width < 700px) {
.table-header {
justify-content: center;
diff --git a/src/client/components/AppDialog.vue b/src/client/components/AppDialog.vue
index 86f9fb1850c47c4dfa5fda3883e81bcc4a50f2a7..df57505b16e236b88af81ee852d69b6c529349c5 100644
--- a/src/client/components/AppDialog.vue
+++ b/src/client/components/AppDialog.vue
@@ -12,7 +12,10 @@
>
<i class="icon-close"></i>
</button>
- <slot />
+
+ <section v-if="isVisible()">
+ <slot />
+ </section>
</dialog>
</template>
diff --git a/src/client/components/TheDownloadPage.vue b/src/client/components/TheDownloadPage.vue
index 8467f5b18f93a164a589f49fd7aab8916a727c2d..5e246495c357c80c2f1b0f05c6dfcc27adbb43e1 100644
--- a/src/client/components/TheDownloadPage.vue
+++ b/src/client/components/TheDownloadPage.vue
@@ -19,7 +19,8 @@
<div
v-else
class="spinner"
- ></div>
+ role="progressbar">
+ </div>
</div>
</template>
diff --git a/src/client/components/TheHomePage.vue b/src/client/components/TheHomePage.vue
index e575d38c33580549caaffa245e49d65dd46208df..d81ccf518dc22630ddbb8faae7d0443b4e35e3a0 100644
--- a/src/client/components/TheHomePage.vue
+++ b/src/client/components/TheHomePage.vue
@@ -124,6 +124,13 @@
</p>
</section>
+ <div class="version-date">
+ Last update:
+ <time :datetime="versionDate">
+ {{ versionDate }}
+ </time>
+ </div>
+
<SearchBar />
<AntibodiesTable v-if="!noResults" />
@@ -140,6 +147,7 @@ import SearchBar from './SearchBar.vue'
const store = useStore()
const noResults = computed(() => { return store.noResults })
+const versionDate = computed(() => { return store.antibodiesVersionDate })
/**
* Fetch the first antibodies on page load in order to
@@ -166,4 +174,12 @@ p {
max-width: 900px;
text-align: justify;
}
+
+.version-date {
+ margin: auto;
+}
+
+.version-date time {
+ font-weight: bold;
+}
</style>
diff --git a/src/client/main.ts b/src/client/main.ts
index a9c4948a07aab662fe74d7240d5055b3a8fb074a..9a2ceab432b938c487e3d09c7b2e135a0a8c019c 100644
--- a/src/client/main.ts
+++ b/src/client/main.ts
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/client/models/APIRequest.ts b/src/client/models/APIRequest.ts
index ba597dc83eda6ae3aa79b418dff188c25d42d0dd..c3197ad4c14579905dc4b21377b618d4a422e086 100644
--- a/src/client/models/APIRequest.ts
+++ b/src/client/models/APIRequest.ts
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 type {
APIFetchParams,
APIFilters,
diff --git a/src/client/router.ts b/src/client/router.ts
index f1c46372de7de2cdf002aca8c986ae14800d2f7f..6636662a552b9e6bd0fbe93da0feded1a5181d01 100644
--- a/src/client/router.ts
+++ b/src/client/router.ts
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/client/store.ts b/src/client/store.ts
index 5d6111d9be0e625db8c7470906e790f82ddeeff4..402666a3012f542cfcdcb98cb0fda0976716f83e 100644
--- a/src/client/store.ts
+++ b/src/client/store.ts
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 type { AxiosError } from 'axios'
import { defineStore } from 'pinia'
import sourceMeta from '../../data/sources.json'
@@ -69,6 +85,15 @@ export const useStore = defineStore('store', {
return Object
.keys(state.statistics?.antibodiesPerLightSegment || {})
.sort(alphanumSort)
+ },
+
+ /**
+ * Get the current version date of the database.
+ * @param state - The state of the store
+ * @returns The version date as an ISO string
+ */
+ antibodiesVersionDate: (state): Statistics['versionDate'] => {
+ return state.statistics?.versionDate.replace(/T.*/, "") || ""
}
},
actions: {
diff --git a/src/client/types.ts b/src/client/types.ts
index b04bbfd1beb492f8ef899512e66dc3e3f3f73006..578ea2206466a6b8784879efda71231e03278212 100644
--- a/src/client/types.ts
+++ b/src/client/types.ts
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 type { APIRequest } from './models/APIRequest'
// Types and interfaces used through the application
@@ -62,6 +78,7 @@ export type SourceMeta = Record<FastaHeader['source'], {
* the application.
*/
export interface Statistics {
+ versionDate: string
antibodies: number
species: Array<Antibody['species']>
sources: Array<FastaHeader['source']>
diff --git a/src/client/utils/alphanumSort.ts b/src/client/utils/alphanumSort.ts
index b03b916909e25f127a8c84f7aab234a811143885..3955a2c0eda3a38585214f0894cd8f799b951602 100644
--- a/src/client/utils/alphanumSort.ts
+++ b/src/client/utils/alphanumSort.ts
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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/>.
+
/**
* A custom strategy to sort the numbers inside a string numerically instead
* of alphabatically.
diff --git a/src/scripts/buildDatabase.js b/src/scripts/buildDatabase.js
index c18da80b4e88e3dcfae7f8f163566e362ec5e3bd..d24fdc8d5eac1c0fedc4d7add88b076f283cec22 100644
--- a/src/scripts/buildDatabase.js
+++ b/src/scripts/buildDatabase.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 buildDatabase from './databaseBuilder.js'
import config from '../server/config/env.js'
diff --git a/src/scripts/databaseBuilder.js b/src/scripts/databaseBuilder.js
index a13774cb5e7f1244c3dc11fb3195835d0c5ad52f..bf19ad4111fe830e899f4bee31b0214a2e20e6a2 100644
--- a/src/scripts/databaseBuilder.js
+++ b/src/scripts/databaseBuilder.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 { createReadStream } from 'node:fs'
import { readdir, readFile } from 'node:fs/promises'
import { dirname, resolve } from 'node:path'
diff --git a/src/scripts/displayStatistics.js b/src/scripts/displayStatistics.js
index b851c867782f07d4324a7d34a247c512a428d5e4..2720c09a4dcba62b7e33870361a100425042d852 100644
--- a/src/scripts/displayStatistics.js
+++ b/src/scripts/displayStatistics.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 buildStatistics from './fastaStatsBuilder.js'
/**
diff --git a/src/scripts/fastaStatsBuilder.js b/src/scripts/fastaStatsBuilder.js
index 873be1644d25bda0de326b6739488f1fc8d98a8f..cb4d76dc9fdcffea27d65bf74d718b999845fa13 100644
--- a/src/scripts/fastaStatsBuilder.js
+++ b/src/scripts/fastaStatsBuilder.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 { createReadStream } from 'node:fs'
import { readdir } from 'node:fs/promises'
import { dirname, resolve } from 'node:path'
diff --git a/src/scripts/fastaValidator.js b/src/scripts/fastaValidator.js
index 0dbf374e836df3e9060aeb9f364eeeaf33e474b9..754927e666d6c556abbab4c6b3c4059b5f418a28 100644
--- a/src/scripts/fastaValidator.js
+++ b/src/scripts/fastaValidator.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 { createReadStream } from 'node:fs'
import { readdir } from 'node:fs/promises'
import { dirname, resolve } from 'node:path'
diff --git a/src/scripts/streams/BuildAntibodiesStream.js b/src/scripts/streams/BuildAntibodiesStream.js
index 5461dbf9a173f83cffeca33fa36faae333d54906..d27a6723288011666aa3295327684c2c9fcf87a4 100644
--- a/src/scripts/streams/BuildAntibodiesStream.js
+++ b/src/scripts/streams/BuildAntibodiesStream.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 { Transform } from "stream";
/**
diff --git a/src/scripts/streams/GenerateHashIdStream.js b/src/scripts/streams/GenerateHashIdStream.js
index 2a70434f0d95a81fcd094f93811f5565524f4b51..d3600f7611464e760c933b4745ea784b846c852b 100644
--- a/src/scripts/streams/GenerateHashIdStream.js
+++ b/src/scripts/streams/GenerateHashIdStream.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 { Transform } from "stream";
import { Antibody } from "../../server/models/Antibody.js";
diff --git a/src/scripts/streams/GroupAntibodiesStream.js b/src/scripts/streams/GroupAntibodiesStream.js
index 7c47e16a114c8dcc0b89fad650b3b64e5507b563..7baffc874231e97df8914edc42d8fc6fcde7e98d 100644
--- a/src/scripts/streams/GroupAntibodiesStream.js
+++ b/src/scripts/streams/GroupAntibodiesStream.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 { Transform } from "stream";
/**
diff --git a/src/scripts/streams/InsertAntibodiesStream.js b/src/scripts/streams/InsertAntibodiesStream.js
index 9ed83b21810bc5362bcea3a6b34187d5b8136a76..1d99b07c659ebfa6d3abde3015b106f25cd422c3 100644
--- a/src/scripts/streams/InsertAntibodiesStream.js
+++ b/src/scripts/streams/InsertAntibodiesStream.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 { MongoClient } from "mongodb";
import { Writable } from "stream";
import config from "../../server/config/env.js";
diff --git a/src/scripts/streams/ParseFastaStream.js b/src/scripts/streams/ParseFastaStream.js
index de3155a3678a04aefc00140ecdf3f93338760036..988892ac88a5f64a055b9a85d44d2e537ec819a6 100644
--- a/src/scripts/streams/ParseFastaStream.js
+++ b/src/scripts/streams/ParseFastaStream.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 { Transform } from "stream"
/**
diff --git a/src/scripts/streams/SanitizeFastaStream.js b/src/scripts/streams/SanitizeFastaStream.js
index c947742a874c5c77c1fb23716178208dabb23c07..ef9130e9452c098bed158ed8ccfceb2586376613 100644
--- a/src/scripts/streams/SanitizeFastaStream.js
+++ b/src/scripts/streams/SanitizeFastaStream.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 { Transform } from "stream";
/**
diff --git a/src/scripts/streams/SplitFastaStream.js b/src/scripts/streams/SplitFastaStream.js
index d7aaf5481a5015dfdb27fbe101290feb82fb755d..0377c5edc19a95319621dbe6d43b1984b67285b3 100644
--- a/src/scripts/streams/SplitFastaStream.js
+++ b/src/scripts/streams/SplitFastaStream.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 { Transform } from "stream";
/**
diff --git a/src/scripts/streams/StatisticsStream.js b/src/scripts/streams/StatisticsStream.js
index 1a68970db2470509a79d804b33f19f7d6e7dcda0..e04e6c727510b2e0bce9b4b2d30b1d4fc5c8876a 100644
--- a/src/scripts/streams/StatisticsStream.js
+++ b/src/scripts/streams/StatisticsStream.js
@@ -1,8 +1,22 @@
+// ABSD
+// Copyright (C) 2025 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 { Writable } from 'node:stream'
import { Antibody } from '../../server/models/Antibody.js'
-// =========================================================================
-
/**
* Build the statistics by incrementing a given stats object.
*/
diff --git a/src/scripts/streams/ValidateFastaStream.js b/src/scripts/streams/ValidateFastaStream.js
index 246364da6dc5e4c1be6443ccd73e9509d48c83bb..f3129581c3f00e9944d640d15e5a2900c535cbab 100644
--- a/src/scripts/streams/ValidateFastaStream.js
+++ b/src/scripts/streams/ValidateFastaStream.js
@@ -1,3 +1,19 @@
+// ABSD
+// Copyright (C) 2025 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 { createHash } from 'crypto';
import { Writable } from 'stream';
diff --git a/src/server/app.js b/src/server/app.js
index 1e0c7913eda6032f357512d87d4d2d9af9f803d2..1670321313ede81f94428628f16459b9bd535325 100644
--- a/src/server/app.js
+++ b/src/server/app.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/config/env.js b/src/server/config/env.js
index df99d1f26b5523d15eebb62a5110388e3a50972e..d467396d818fc2ff58791fb0cec3239010782198 100644
--- a/src/server/config/env.js
+++ b/src/server/config/env.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
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/hooks/buildDBQuery.js b/src/server/hooks/buildDBQuery.js
index 6e28c1cb5aac3e1970fdaaab0c8065ff9147efda..f63af6644fff4e80ae581fa4a451ed8542763ced 100644
--- a/src/server/hooks/buildDBQuery.js
+++ b/src/server/hooks/buildDBQuery.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/hooks/parseRequest.js b/src/server/hooks/parseRequest.js
index a63bc84233f294436d62970c1adf19a4853a9906..a5274b49d6b5336a8ce7ff0870957fce253ffac9 100644
--- a/src/server/hooks/parseRequest.js
+++ b/src/server/hooks/parseRequest.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/models/Antibody.js b/src/server/models/Antibody.js
index 8c8e67b869f63ed729d58197335f813ca7f9e581..67fddcb2b8e3cff2b86068b0526f549210c758cc 100644
--- a/src/server/models/Antibody.js
+++ b/src/server/models/Antibody.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
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/models/AntibodyFastaStream.js b/src/server/models/AntibodyFastaStream.js
index 2e1f61a707868267b91df05e2f84252a6cb289b7..87bcaa56d6eaa975ca96f851c89f6b0fdd6d3af5 100644
--- a/src/server/models/AntibodyFastaStream.js
+++ b/src/server/models/AntibodyFastaStream.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/models/AntibodyJsonStream.js b/src/server/models/AntibodyJsonStream.js
index 72f55865b26dd744dc1c8e31c451c2f8df38eef7..8e7a65df4a6ca1f94338990a2941b4c78965bfaa 100644
--- a/src/server/models/AntibodyJsonStream.js
+++ b/src/server/models/AntibodyJsonStream.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/models/ArchiveBuilder.js b/src/server/models/ArchiveBuilder.js
index aa13d4035c7073dfa0845e71198e8ff50fa66d9e..bb25b8d9afc5f177e206e8d48575e54eefe7f6a4 100644
--- a/src/server/models/ArchiveBuilder.js
+++ b/src/server/models/ArchiveBuilder.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/models/ArchiveJobs.js b/src/server/models/ArchiveJobs.js
index 2b36e13263cd56981f7dcd08f7abce2acb12eb0b..e7cb91cafca471ba009067dbb159b17bd93071b7 100644
--- a/src/server/models/ArchiveJobs.js
+++ b/src/server/models/ArchiveJobs.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/models/Statistics.js b/src/server/models/Statistics.js
index d38b5122266020350fe70af4b80ce3b7699c3376..abb570e97c1b2024201cce39bf6fc306dbb2b960 100644
--- a/src/server/models/Statistics.js
+++ b/src/server/models/Statistics.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
@@ -18,6 +18,7 @@
* Statistics about the antibodies.
*/
export class Statistics {
+ versionDate = ""
antibodies = 0
species = new Set()
sources = new Set()
diff --git a/src/server/routes/antibodiesCountRoute.js b/src/server/routes/antibodiesCountRoute.js
index 26431d1a56e77f4b96974d6e771cab8a70a24572..b16992233c60dd459e032fbeb76a65ebeb998fde 100644
--- a/src/server/routes/antibodiesCountRoute.js
+++ b/src/server/routes/antibodiesCountRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/antibodiesDownloadArchiveFileRoute.js b/src/server/routes/antibodiesDownloadArchiveFileRoute.js
index 684e23d6054ae34320c4608ac9c2d65c31fb553f..865899876a20b944b7f949cc39d2b1b56cd48ade 100644
--- a/src/server/routes/antibodiesDownloadArchiveFileRoute.js
+++ b/src/server/routes/antibodiesDownloadArchiveFileRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/antibodiesDownloadArchiveRoute.js b/src/server/routes/antibodiesDownloadArchiveRoute.js
index 25349e0d189ffdf62376b06503b99d270a050157..acc3e8b22ca45d4b51155c0a3c4f55d11cd4f974 100644
--- a/src/server/routes/antibodiesDownloadArchiveRoute.js
+++ b/src/server/routes/antibodiesDownloadArchiveRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/antibodiesDownloadRoute.js b/src/server/routes/antibodiesDownloadRoute.js
index 5b2b933695b02b4acbc0b931987faa593b2842dc..4163910822c747d9a8d0b53f36aab1f98ee09aeb 100644
--- a/src/server/routes/antibodiesDownloadRoute.js
+++ b/src/server/routes/antibodiesDownloadRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/antibodiesFindByIdRoute.js b/src/server/routes/antibodiesFindByIdRoute.js
index 975b81a785b7dff2e00349c5c45f5cab5ed3982f..63bbeead56bff56ae9c90626ee97df85c92431e0 100644
--- a/src/server/routes/antibodiesFindByIdRoute.js
+++ b/src/server/routes/antibodiesFindByIdRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/antibodiesFindRoute.js b/src/server/routes/antibodiesFindRoute.js
index d4e3b5ca7f5af99619b90893b7503b50e04b10b8..30e649181320a5e4591a79b8ad647f0edffa8226 100644
--- a/src/server/routes/antibodiesFindRoute.js
+++ b/src/server/routes/antibodiesFindRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/antibodiesSourcesRoute.js b/src/server/routes/antibodiesSourcesRoute.js
index 182ba6ac4ba412fb0470b41ce6f8360231ccf222..d55ec2e96f631e8c53e3612f360273371c651c3d 100644
--- a/src/server/routes/antibodiesSourcesRoute.js
+++ b/src/server/routes/antibodiesSourcesRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/antibodiesSpeciesRoute.js b/src/server/routes/antibodiesSpeciesRoute.js
index 91934e8fa932bf5461e24bb0ae474d2b86346485..8b5373240d33912efbb4ffe14dbbdece6341564a 100644
--- a/src/server/routes/antibodiesSpeciesRoute.js
+++ b/src/server/routes/antibodiesSpeciesRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/antibodiesVGeneSegmentsRoute.js b/src/server/routes/antibodiesVGeneSegmentsRoute.js
index 19162c4dca06de3c2d4046bd4aca19c387146f85..b6b3ae72d3f6308a5e3c04002e3036bd3fd2ac74 100644
--- a/src/server/routes/antibodiesVGeneSegmentsRoute.js
+++ b/src/server/routes/antibodiesVGeneSegmentsRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/downloadsFileRoute.js b/src/server/routes/downloadsFileRoute.js
index 93e5c6af602a03a3e6d9054ab63951774131aef6..aa5479894ca317d179c9657ebad741aa6dbf0282 100644
--- a/src/server/routes/downloadsFileRoute.js
+++ b/src/server/routes/downloadsFileRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/downloadsRoute.js b/src/server/routes/downloadsRoute.js
index 39c4bb2389c26ac13f43e4dec2a0f67c5edf1f9a..a9af8157ac8152e387fa6d30a555d4acf8193aac 100644
--- a/src/server/routes/downloadsRoute.js
+++ b/src/server/routes/downloadsRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/healthCheckRoute.js b/src/server/routes/healthCheckRoute.js
index 02a546a8824f8010a67bcbcdde56e68fb031da33..cb7404da3b0c5c1eefe13ad4e03e248277636828 100644
--- a/src/server/routes/healthCheckRoute.js
+++ b/src/server/routes/healthCheckRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/readyCheckRoute.js b/src/server/routes/readyCheckRoute.js
index 2ec8df6c46b393ef58917fe78b819191a7955d28..2b59e122d15bc4dbed277a84d9f46cde57b6da7d 100644
--- a/src/server/routes/readyCheckRoute.js
+++ b/src/server/routes/readyCheckRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/routes/statisticsRoute.js b/src/server/routes/statisticsRoute.js
index ebf884c74f9c29cb27881abe92350474b87d5873..7edee683adaab1b10afe66fb602a094774dce697 100644
--- a/src/server/routes/statisticsRoute.js
+++ b/src/server/routes/statisticsRoute.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/utils/archiveBuilderWorker.js b/src/server/utils/archiveBuilderWorker.js
index a13de23a6abbe5868686b45c24d69ce2a5994931..2b59c38934344b6a895b33fe5673b655d27a2c05 100644
--- a/src/server/utils/archiveBuilderWorker.js
+++ b/src/server/utils/archiveBuilderWorker.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/utils/databaseIsSync.js b/src/server/utils/databaseIsSync.js
index fbeaacf1f0ea23d2ea6f18ca859642ec989ae9ff..a35cc44440b6d50a1d96d2e2a5f85600a0a18380 100644
--- a/src/server/utils/databaseIsSync.js
+++ b/src/server/utils/databaseIsSync.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
diff --git a/src/server/utils/escapeString.js b/src/server/utils/escapeString.js
index 2d06104b1da8fbdfed68b48c3927849737ada7dc..c64b7f6460e759a47d9215e22b76295b7780285b 100644
--- a/src/server/utils/escapeString.js
+++ b/src/server/utils/escapeString.js
@@ -1,5 +1,5 @@
// ABSD
-// Copyright (C) 2023 Institut Pasteur
+// Copyright (C) 2025 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
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..3bdd5fe50f1706e4186a71709382434ba240f19c 100644
--- a/vite.config.ts
+++ b/vite.config.ts
@@ -1,4 +1,3 @@
-/// <reference types='vitest' />
import { defineConfig } from 'vite'
import vue from '@vitejs/plugin-vue'
import brotliPlugin from 'rollup-plugin-brotli'
@@ -30,11 +29,5 @@ 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']
}
})