diff --git a/Dockerfile b/Dockerfile
index 9562cdf5dad7fe1406a65d9dc73f1dc81378e6bf..8805e9642b765f9f45cf65ef59ed735739f1d2a9 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -31,12 +31,11 @@ LABEL name="absd" \
# Copy only the relevant files
COPY --from=builder /usr/build/src/server ./src/server
+COPY --from=builder /usr/build/src/scripts ./src/scripts
COPY --from=builder /usr/build/dist/ ./dist/
COPY --from=builder /usr/build/package.json ./package.json
COPY --from=builder /usr/build/package-lock.json ./package-lock.json
COPY ./data/ ./data/
-# Scripts are needed to build the database if there is none
-COPY ./scripts/ ./scripts/
# Install production dependencies and remove the cache for extra space saving
RUN npm ci && npm cache clean --force
diff --git a/biome.json b/biome.json
index 18bef1a36cfcc583c7d450793864abd1d69658bd..b724216311f220e92778bda923ac76e7ed274393 100644
--- a/biome.json
+++ b/biome.json
@@ -21,7 +21,8 @@
"rules": {
"recommended": true,
"complexity": {
- "noForEach": "off"
+ "noForEach": "off",
+ "useArrowFunction": "off"
}
}
}
diff --git a/data/2024-09-21-stats.json b/data/2024-09-21-stats.json
index 3a4842ccc1323111f5e151b1afc55e570d97e2fc..4eee69e6bf05cd23c61f8ad279b55acfcd4ad53e 100644
--- a/data/2024-09-21-stats.json
+++ b/data/2024-09-21-stats.json
@@ -40,7 +40,7 @@
"CoV-AbDab-PDB": 331,
"EBOLA": 294
},
- "antibodiesPerHeavySegments": {
+ "antibodiesPerHeavySegment": {
"IGHV1": 114950,
"IGHV3": 405509,
"IGHV4": 173337,
@@ -57,7 +57,7 @@
"IGHV11": 10,
"IGHV15": 4
},
- "antibodiesPerLightSegments": {
+ "antibodiesPerLightSegment": {
"IGLV8": 6932,
"IGLV6": 7105,
"IGKV3": 165916,
diff --git a/data/2024-12-03-stats.json b/data/2024-12-03-stats.json
index 626fc71b43c0ab189a7e4f989afbade01d1daffa..5180df8b03a124c8ee87293e3eba7c8d2a531dcd 100644
--- a/data/2024-12-03-stats.json
+++ b/data/2024-12-03-stats.json
@@ -50,7 +50,7 @@
"OAS": 708308,
"UNIPROT": 1822
},
- "antibodiesPerHeavySegments": {
+ "antibodiesPerHeavySegment": {
"IGHV1": 231581,
"IGHV2": 50537,
"IGHV3": 679756,
@@ -67,7 +67,7 @@
"IGHV12": 32,
"IGHV15": 14
},
- "antibodiesPerLightSegments": {
+ "antibodiesPerLightSegment": {
"IGKV4": 96494,
"IGLV11": 31,
"IGLV8": 10559,
diff --git a/data/2024-12-23-stats.json b/data/2024-12-23-stats.json
index 3d978b72c49948bc9257bd9dfa3bccd3c8fb2d17..ec864cf830db68b068c7e0b799c65642326aef6a 100644
--- a/data/2024-12-23-stats.json
+++ b/data/2024-12-23-stats.json
@@ -50,7 +50,7 @@
"UNIPROT": 1822,
"EBOLA": 282
},
- "antibodiesPerHeavySegments": {
+ "antibodiesPerHeavySegment": {
"IGHV7": 10884,
"IGHV4": 296316,
"IGHV1": 231576,
@@ -67,7 +67,7 @@
"IGHV15": 14,
"IGHV12": 32
},
- "antibodiesPerLightSegments": {
+ "antibodiesPerLightSegment": {
"IGLV7": 18156,
"IGLV1": 152339,
"IGKV2": 93389,
diff --git a/k8s/absd.yaml b/k8s/absd.yaml
index ab68a7ef6d2283895a8947ca5c9101b796792c02..0886fd57178dc80e9627331a4b59d54c1d2ed795 100644
--- a/k8s/absd.yaml
+++ b/k8s/absd.yaml
@@ -9,7 +9,7 @@ spec:
- ReadWriteMany
resources:
requests:
- storage: 10Gi
+ storage: 20Gi
storageClassName: ceph-fs
---
apiVersion: apps/v1
diff --git a/package-lock.json b/package-lock.json
index 44a3bf77b430055e8e614a3d1223c28ffa2ffe57..16d08d9f8734d7c892174fd60609bea89aa34372 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -9,35 +9,35 @@
"version": "1.0.0",
"license": "GPL-3.0",
"dependencies": {
- "@fastify/mongodb": "^9.0.1",
- "@fastify/static": "^8.0.3",
+ "@fastify/mongodb": "^9.0.2",
+ "@fastify/static": "^8.0.4",
"axios": "^1.7.9",
- "env-schema": "^6.0.0",
- "fastify": "^5.1.0",
+ "env-schema": "^6.0.1",
+ "fastify": "^5.2.1",
"modern-normalize": "^3.0.1",
- "mongodb": "^6.11.0",
- "pinia": "^2.3.0",
- "plotly.js-dist-min": "^2.35.2",
- "qs": "^6.13.1",
+ "mongodb": "^6.12.0",
+ "pinia": "^2.3.1",
+ "plotly.js-dist-min": "^2.35.3",
+ "qs": "^6.14.0",
"vue": "^3.5.13",
"vue-router": "^4.5.0"
},
"devDependencies": {
"@biomejs/biome": "^1.9.4",
- "@types/node": "^22.10.1",
+ "@types/node": "^22.10.9",
"@types/plotly.js-dist-min": "^2.3.4",
- "@types/qs": "^6.9.17",
+ "@types/qs": "^6.9.18",
"@vitejs/plugin-vue": "^5.2.1",
"autoprefixer": "^10.4.20",
- "concurrently": "^9.1.0",
+ "concurrently": "^9.1.2",
"cssnano": "^7.0.6",
- "nodemon": "^3.1.7",
+ "nodemon": "^3.1.9",
"pino-pretty": "^13.0.0",
"rollup-plugin-brotli": "^3.1.0",
"rollup-plugin-gzip": "^4.0.1",
- "typescript": "^5.6.3",
- "vite": "^6.0.3",
- "vue-tsc": "^2.1.10"
+ "typescript": "^5.7.3",
+ "vite": "^6.0.11",
+ "vue-tsc": "^2.2.0"
}
},
"node_modules/@babel/helper-string-parser": {
@@ -251,9 +251,9 @@
}
},
"node_modules/@esbuild/aix-ppc64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/aix-ppc64/-/aix-ppc64-0.24.0.tgz",
- "integrity": "sha512-WtKdFM7ls47zkKHFVzMz8opM7LkcsIp9amDUBIAWirg70RM71WRSjdILPsY5Uv1D42ZpUfaPILDlfactHgsRkw==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/aix-ppc64/-/aix-ppc64-0.24.2.tgz",
+ "integrity": "sha512-thpVCb/rhxE/BnMLQ7GReQLLN8q9qbHmI55F4489/ByVg2aQaQ6kbcLb6FHkocZzQhxc4gx0sCk0tJkKBFzDhA==",
"cpu": [
"ppc64"
],
@@ -268,9 +268,9 @@
}
},
"node_modules/@esbuild/android-arm": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/android-arm/-/android-arm-0.24.0.tgz",
- "integrity": "sha512-arAtTPo76fJ/ICkXWetLCc9EwEHKaeya4vMrReVlEIUCAUncH7M4bhMQ+M9Vf+FFOZJdTNMXNBrWwW+OXWpSew==",
+ "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==",
"cpu": [
"arm"
],
@@ -285,9 +285,9 @@
}
},
"node_modules/@esbuild/android-arm64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/android-arm64/-/android-arm64-0.24.0.tgz",
- "integrity": "sha512-Vsm497xFM7tTIPYK9bNTYJyF/lsP590Qc1WxJdlB6ljCbdZKU9SY8i7+Iin4kyhV/KV5J2rOKsBQbB77Ab7L/w==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/android-arm64/-/android-arm64-0.24.2.tgz",
+ "integrity": "sha512-cNLgeqCqV8WxfcTIOeL4OAtSmL8JjcN6m09XIgro1Wi7cF4t/THaWEa7eL5CMoMBdjoHOTh/vwTO/o2TRXIyzg==",
"cpu": [
"arm64"
],
@@ -302,9 +302,9 @@
}
},
"node_modules/@esbuild/android-x64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/android-x64/-/android-x64-0.24.0.tgz",
- "integrity": "sha512-t8GrvnFkiIY7pa7mMgJd7p8p8qqYIz1NYiAoKc75Zyv73L3DZW++oYMSHPRarcotTKuSs6m3hTOa5CKHaS02TQ==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/android-x64/-/android-x64-0.24.2.tgz",
+ "integrity": "sha512-B6Q0YQDqMx9D7rvIcsXfmJfvUYLoP722bgfBlO5cGvNVb5V/+Y7nhBE3mHV9OpxBf4eAS2S68KZztiPaWq4XYw==",
"cpu": [
"x64"
],
@@ -319,9 +319,9 @@
}
},
"node_modules/@esbuild/darwin-arm64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/darwin-arm64/-/darwin-arm64-0.24.0.tgz",
- "integrity": "sha512-CKyDpRbK1hXwv79soeTJNHb5EiG6ct3efd/FTPdzOWdbZZfGhpbcqIpiD0+vwmpu0wTIL97ZRPZu8vUt46nBSw==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/darwin-arm64/-/darwin-arm64-0.24.2.tgz",
+ "integrity": "sha512-kj3AnYWc+CekmZnS5IPu9D+HWtUI49hbnyqk0FLEJDbzCIQt7hg7ucF1SQAilhtYpIujfaHr6O0UHlzzSPdOeA==",
"cpu": [
"arm64"
],
@@ -336,9 +336,9 @@
}
},
"node_modules/@esbuild/darwin-x64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/darwin-x64/-/darwin-x64-0.24.0.tgz",
- "integrity": "sha512-rgtz6flkVkh58od4PwTRqxbKH9cOjaXCMZgWD905JOzjFKW+7EiUObfd/Kav+A6Gyud6WZk9w+xu6QLytdi2OA==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/darwin-x64/-/darwin-x64-0.24.2.tgz",
+ "integrity": "sha512-WeSrmwwHaPkNR5H3yYfowhZcbriGqooyu3zI/3GGpF8AyUdsrrP0X6KumITGA9WOyiJavnGZUwPGvxvwfWPHIA==",
"cpu": [
"x64"
],
@@ -353,9 +353,9 @@
}
},
"node_modules/@esbuild/freebsd-arm64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/freebsd-arm64/-/freebsd-arm64-0.24.0.tgz",
- "integrity": "sha512-6Mtdq5nHggwfDNLAHkPlyLBpE5L6hwsuXZX8XNmHno9JuL2+bg2BX5tRkwjyfn6sKbxZTq68suOjgWqCicvPXA==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/freebsd-arm64/-/freebsd-arm64-0.24.2.tgz",
+ "integrity": "sha512-UN8HXjtJ0k/Mj6a9+5u6+2eZ2ERD7Edt1Q9IZiB5UZAIdPnVKDoG7mdTVGhHJIeEml60JteamR3qhsr1r8gXvg==",
"cpu": [
"arm64"
],
@@ -370,9 +370,9 @@
}
},
"node_modules/@esbuild/freebsd-x64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/freebsd-x64/-/freebsd-x64-0.24.0.tgz",
- "integrity": "sha512-D3H+xh3/zphoX8ck4S2RxKR6gHlHDXXzOf6f/9dbFt/NRBDIE33+cVa49Kil4WUjxMGW0ZIYBYtaGCa2+OsQwQ==",
+ "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==",
"cpu": [
"x64"
],
@@ -387,9 +387,9 @@
}
},
"node_modules/@esbuild/linux-arm": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-arm/-/linux-arm-0.24.0.tgz",
- "integrity": "sha512-gJKIi2IjRo5G6Glxb8d3DzYXlxdEj2NlkixPsqePSZMhLudqPhtZ4BUrpIuTjJYXxvF9njql+vRjB2oaC9XpBw==",
+ "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==",
"cpu": [
"arm"
],
@@ -404,9 +404,9 @@
}
},
"node_modules/@esbuild/linux-arm64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-arm64/-/linux-arm64-0.24.0.tgz",
- "integrity": "sha512-TDijPXTOeE3eaMkRYpcy3LarIg13dS9wWHRdwYRnzlwlA370rNdZqbcp0WTyyV/k2zSxfko52+C7jU5F9Tfj1g==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-arm64/-/linux-arm64-0.24.2.tgz",
+ "integrity": "sha512-7HnAD6074BW43YvvUmE/35Id9/NB7BeX5EoNkK9obndmZBUk8xmJJeU7DwmUeN7tkysslb2eSl6CTrYz6oEMQg==",
"cpu": [
"arm64"
],
@@ -421,9 +421,9 @@
}
},
"node_modules/@esbuild/linux-ia32": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-ia32/-/linux-ia32-0.24.0.tgz",
- "integrity": "sha512-K40ip1LAcA0byL05TbCQ4yJ4swvnbzHscRmUilrmP9Am7//0UjPreh4lpYzvThT2Quw66MhjG//20mrufm40mA==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-ia32/-/linux-ia32-0.24.2.tgz",
+ "integrity": "sha512-sfv0tGPQhcZOgTKO3oBE9xpHuUqguHvSo4jl+wjnKwFpapx+vUDcawbwPNuBIAYdRAvIDBfZVvXprIj3HA+Ugw==",
"cpu": [
"ia32"
],
@@ -438,9 +438,9 @@
}
},
"node_modules/@esbuild/linux-loong64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-loong64/-/linux-loong64-0.24.0.tgz",
- "integrity": "sha512-0mswrYP/9ai+CU0BzBfPMZ8RVm3RGAN/lmOMgW4aFUSOQBjA31UP8Mr6DDhWSuMwj7jaWOT0p0WoZ6jeHhrD7g==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-loong64/-/linux-loong64-0.24.2.tgz",
+ "integrity": "sha512-CN9AZr8kEndGooS35ntToZLTQLHEjtVB5n7dl8ZcTZMonJ7CCfStrYhrzF97eAecqVbVJ7APOEe18RPI4KLhwQ==",
"cpu": [
"loong64"
],
@@ -455,9 +455,9 @@
}
},
"node_modules/@esbuild/linux-mips64el": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-mips64el/-/linux-mips64el-0.24.0.tgz",
- "integrity": "sha512-hIKvXm0/3w/5+RDtCJeXqMZGkI2s4oMUGj3/jM0QzhgIASWrGO5/RlzAzm5nNh/awHE0A19h/CvHQe6FaBNrRA==",
+ "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==",
"cpu": [
"mips64el"
],
@@ -472,9 +472,9 @@
}
},
"node_modules/@esbuild/linux-ppc64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-ppc64/-/linux-ppc64-0.24.0.tgz",
- "integrity": "sha512-HcZh5BNq0aC52UoocJxaKORfFODWXZxtBaaZNuN3PUX3MoDsChsZqopzi5UupRhPHSEHotoiptqikjN/B77mYQ==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-ppc64/-/linux-ppc64-0.24.2.tgz",
+ "integrity": "sha512-shsVrgCZ57Vr2L8mm39kO5PPIb+843FStGt7sGGoqiiWYconSxwTiuswC1VJZLCjNiMLAMh34jg4VSEQb+iEbw==",
"cpu": [
"ppc64"
],
@@ -489,9 +489,9 @@
}
},
"node_modules/@esbuild/linux-riscv64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-riscv64/-/linux-riscv64-0.24.0.tgz",
- "integrity": "sha512-bEh7dMn/h3QxeR2KTy1DUszQjUrIHPZKyO6aN1X4BCnhfYhuQqedHaa5MxSQA/06j3GpiIlFGSsy1c7Gf9padw==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-riscv64/-/linux-riscv64-0.24.2.tgz",
+ "integrity": "sha512-4eSFWnU9Hhd68fW16GD0TINewo1L6dRrB+oLNNbYyMUAeOD2yCK5KXGK1GH4qD/kT+bTEXjsyTCiJGHPZ3eM9Q==",
"cpu": [
"riscv64"
],
@@ -506,9 +506,9 @@
}
},
"node_modules/@esbuild/linux-s390x": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-s390x/-/linux-s390x-0.24.0.tgz",
- "integrity": "sha512-ZcQ6+qRkw1UcZGPyrCiHHkmBaj9SiCD8Oqd556HldP+QlpUIe2Wgn3ehQGVoPOvZvtHm8HPx+bH20c9pvbkX3g==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-s390x/-/linux-s390x-0.24.2.tgz",
+ "integrity": "sha512-S0Bh0A53b0YHL2XEXC20bHLuGMOhFDO6GN4b3YjRLK//Ep3ql3erpNcPlEFed93hsQAjAQDNsvcK+hV90FubSw==",
"cpu": [
"s390x"
],
@@ -523,9 +523,9 @@
}
},
"node_modules/@esbuild/linux-x64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/linux-x64/-/linux-x64-0.24.0.tgz",
- "integrity": "sha512-vbutsFqQ+foy3wSSbmjBXXIJ6PL3scghJoM8zCL142cGaZKAdCZHyf+Bpu/MmX9zT9Q0zFBVKb36Ma5Fzfa8xA==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/linux-x64/-/linux-x64-0.24.2.tgz",
+ "integrity": "sha512-8Qi4nQcCTbLnK9WoMjdC9NiTG6/E38RNICU6sUNqK0QFxCYgoARqVqxdFmWkdonVsvGqWhmm7MO0jyTqLqwj0Q==",
"cpu": [
"x64"
],
@@ -539,10 +539,27 @@
"node": ">=18"
}
},
+ "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==",
+ "cpu": [
+ "arm64"
+ ],
+ "dev": true,
+ "license": "MIT",
+ "optional": true,
+ "os": [
+ "netbsd"
+ ],
+ "engines": {
+ "node": ">=18"
+ }
+ },
"node_modules/@esbuild/netbsd-x64": {
- "version": "0.24.0",
- "resolved": "https://registry.npmjs.org/@esbuild/netbsd-x64/-/netbsd-x64-0.24.0.tgz",
- "integrity": "sha512-hjQ0R/ulkO8fCYFsG0FZoH+pWgTTDreqpqY7UnQntnaKv95uP5iW3+dChxnx7C3trQQU40S+OgWhUVwCjVFLvg==",
+ "version": "0.24.2",
+ "resolved": "https://registry.npmjs.org/@esbuild/netbsd-x64/-/netbsd-x64-0.24.2.tgz",
+ "integrity": "sha512-VefFaQUc4FMmJuAxmIHgUmfNiLXY438XrL4GDNV1Y1H/RW3qow68xTwjZKfj/+Plp9NANmzbH5R40Meudu8mmw==",
"cpu": [
"x64"
],
@@ -557,9 +574,9 @@
}
},
"node_modules/@esbuild/openbsd-arm64": {
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- "resolved": "https://registry.npmjs.org/@esbuild/openbsd-arm64/-/openbsd-arm64-0.24.0.tgz",
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+ "version": "1.0.1",
+ "resolved": "https://registry.npmjs.org/side-channel-map/-/side-channel-map-1.0.1.tgz",
+ "integrity": "sha512-VCjCNfgMsby3tTdo02nbjtM/ewra6jPHmpThenkTYh8pG9ucZ/1P8So4u4FGBek/BjpOVsDCMoLA/iuBKIFXRA==",
+ "license": "MIT",
+ "dependencies": {
+ "call-bound": "^1.0.2",
+ "es-errors": "^1.3.0",
+ "get-intrinsic": "^1.2.5",
+ "object-inspect": "^1.13.3"
+ },
+ "engines": {
+ "node": ">= 0.4"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ljharb"
+ }
+ },
+ "node_modules/side-channel-weakmap": {
+ "version": "1.0.2",
+ "resolved": "https://registry.npmjs.org/side-channel-weakmap/-/side-channel-weakmap-1.0.2.tgz",
+ "integrity": "sha512-WPS/HvHQTYnHisLo9McqBHOJk2FkHO/tlpvldyrnem4aeQp4hai3gythswg6p01oSoTl58rcpiFAjF2br2Ak2A==",
+ "license": "MIT",
+ "dependencies": {
+ "call-bound": "^1.0.2",
+ "es-errors": "^1.3.0",
+ "get-intrinsic": "^1.2.5",
+ "object-inspect": "^1.13.3",
+ "side-channel-map": "^1.0.1"
},
"engines": {
"node": ">= 0.4"
@@ -4558,9 +4674,9 @@
"dev": true
},
"node_modules/typescript": {
- "version": "5.6.3",
- "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.6.3.tgz",
- "integrity": "sha512-hjcS1mhfuyi4WW8IWtjP7brDrG2cuDZukyrYrSauoXGNgx0S7zceP07adYkJycEr56BOUTNPzbInooiN3fn1qw==",
+ "version": "5.7.3",
+ "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.7.3.tgz",
+ "integrity": "sha512-84MVSjMEHP+FQRPy3pX9sTVV/INIex71s9TL2Gm5FG/WG1SqXeKyZ0k7/blY/4FdOzI12CBy1vGc4og/eus0fw==",
"devOptional": true,
"license": "Apache-2.0",
"bin": {
@@ -4629,13 +4745,13 @@
"dev": true
},
"node_modules/vite": {
- "version": "6.0.3",
- "resolved": "https://registry.npmjs.org/vite/-/vite-6.0.3.tgz",
- "integrity": "sha512-Cmuo5P0ENTN6HxLSo6IHsjCLn/81Vgrp81oaiFFMRa8gGDj5xEjIcEpf2ZymZtZR8oU0P2JX5WuUp/rlXcHkAw==",
+ "version": "6.0.11",
+ "resolved": "https://registry.npmjs.org/vite/-/vite-6.0.11.tgz",
+ "integrity": "sha512-4VL9mQPKoHy4+FE0NnRE/kbY51TOfaknxAjt3fJbGJxhIpBZiqVzlZDEesWWsuREXHwNdAoOFZ9MkPEVXczHwg==",
"dev": true,
"license": "MIT",
"dependencies": {
- "esbuild": "^0.24.0",
+ "esbuild": "^0.24.2",
"postcss": "^8.4.49",
"rollup": "^4.23.0"
},
@@ -4744,15 +4860,14 @@
}
},
"node_modules/vue-tsc": {
- "version": "2.1.10",
- "resolved": "https://registry.npmjs.org/vue-tsc/-/vue-tsc-2.1.10.tgz",
- "integrity": "sha512-RBNSfaaRHcN5uqVqJSZh++Gy/YUzryuv9u1aFWhsammDJXNtUiJMNoJ747lZcQ68wUQFx6E73y4FY3D8E7FGMA==",
+ "version": "2.2.0",
+ "resolved": "https://registry.npmjs.org/vue-tsc/-/vue-tsc-2.2.0.tgz",
+ "integrity": "sha512-gtmM1sUuJ8aSb0KoAFmK9yMxb8TxjewmxqTJ1aKphD5Cbu0rULFY6+UQT51zW7SpUcenfPUuflKyVwyx9Qdnxg==",
"dev": true,
"license": "MIT",
"dependencies": {
- "@volar/typescript": "~2.4.8",
- "@vue/language-core": "2.1.10",
- "semver": "^7.5.4"
+ "@volar/typescript": "~2.4.11",
+ "@vue/language-core": "2.2.0"
},
"bin": {
"vue-tsc": "bin/vue-tsc.js"
diff --git a/package.json b/package.json
index 031254e5a22d3d22ff7943bf357c8c0ded36c5cd..ca2a2f5190353ddd842c05438477a5d435857898 100644
--- a/package.json
+++ b/package.json
@@ -10,9 +10,9 @@
"dev:client": "vite",
"dev:server": "nodemon --use-strict src/server/app.js | pino-pretty -t 'yyyy-mm-dd HH:MM:ss'",
"build": "vue-tsc && vite build",
- "build:db": "node scripts/buildDatabase.js",
- "stats": "node scripts/buildStatistics",
- "validate": "node scripts/fastaValidator.js",
+ "build:db": "node src/scripts/buildDatabase.js",
+ "stats": "node src/scripts/displayStatistics",
+ "validate": "node src/scripts/fastaValidator.js",
"lint": "npm run lint:client; npm run lint:server",
"lint:fix": "npm run lint:client:fix; npm run lint:server:fix",
"lint:client": "biome check src/client",
@@ -28,34 +28,34 @@
"author": "Simon Malesys",
"license": "GPL-3.0",
"dependencies": {
- "@fastify/mongodb": "^9.0.1",
- "@fastify/static": "^8.0.3",
+ "@fastify/mongodb": "^9.0.2",
+ "@fastify/static": "^8.0.4",
"axios": "^1.7.9",
- "env-schema": "^6.0.0",
- "fastify": "^5.1.0",
+ "env-schema": "^6.0.1",
+ "fastify": "^5.2.1",
"modern-normalize": "^3.0.1",
- "mongodb": "^6.11.0",
- "pinia": "^2.3.0",
- "plotly.js-dist-min": "^2.35.2",
- "qs": "^6.13.1",
+ "mongodb": "^6.12.0",
+ "pinia": "^2.3.1",
+ "plotly.js-dist-min": "^2.35.3",
+ "qs": "^6.14.0",
"vue": "^3.5.13",
"vue-router": "^4.5.0"
},
"devDependencies": {
"@biomejs/biome": "^1.9.4",
- "@types/node": "^22.10.1",
+ "@types/node": "^22.10.9",
"@types/plotly.js-dist-min": "^2.3.4",
- "@types/qs": "^6.9.17",
+ "@types/qs": "^6.9.18",
"@vitejs/plugin-vue": "^5.2.1",
"autoprefixer": "^10.4.20",
- "concurrently": "^9.1.0",
+ "concurrently": "^9.1.2",
"cssnano": "^7.0.6",
- "nodemon": "^3.1.7",
+ "nodemon": "^3.1.9",
"pino-pretty": "^13.0.0",
"rollup-plugin-brotli": "^3.1.0",
"rollup-plugin-gzip": "^4.0.1",
- "typescript": "^5.6.3",
- "vite": "^6.0.3",
- "vue-tsc": "^2.1.10"
+ "typescript": "^5.7.3",
+ "vite": "^6.0.11",
+ "vue-tsc": "^2.2.0"
}
}
diff --git a/scripts/antibodySchema.json b/scripts/antibodySchema.json
deleted file mode 100644
index 2402bc28624d9501c7e9627647615d9caaf04dfd..0000000000000000000000000000000000000000
--- a/scripts/antibodySchema.json
+++ /dev/null
@@ -1,95 +0,0 @@
-{
- "$jsonSchema": {
- "title": "Antibody validation schema",
- "required": [
- "_id",
- "id",
- "species",
- "heavyChain",
- "lightChain"
- ],
- "additionalProperties": false,
- "properties": {
- "_id": {
- "bsonType": "objectId"
- },
- "id": {
- "bsonType": "string"
- },
- "hashId": {
- "bsonType": "string"
- },
- "species": {
- "bsonType": "string"
- },
- "heavyChain": {
- "bsonType": "object",
- "properties": {
- "headers": {
- "bsonType": "array",
- "items": {
- "bsonType": "object",
- "properties": {
- "id": {
- "bsonType": "string"
- },
- "source": {
- "bsonType": "string"
- },
- "header": {
- "bsonType": "string"
- }
- },
- "required": [
- "id",
- "source",
- "header"
- ],
- "additionalProperties": false
- }
- },
- "sequence": {
- "bsonType": "string"
- },
- "rawFasta": {
- "bsonType": "string"
- }
- }
- },
- "lightChain": {
- "bsonType": "object",
- "properties": {
- "headers": {
- "bsonType": "array",
- "items": {
- "bsonType": "object",
- "properties": {
- "id": {
- "bsonType": "string"
- },
- "source": {
- "bsonType": "string"
- },
- "header": {
- "bsonType": "string"
- }
- },
- "required": [
- "id",
- "source",
- "header"
- ],
- "additionalProperties": false
- }
- },
- "sequence": {
- "bsonType": "string"
- },
- "rawFasta": {
- "bsonType": "string"
- }
- }
- }
- }
- }
-}
diff --git a/scripts/buildStatistics.js b/scripts/buildStatistics.js
deleted file mode 100644
index 3b63f8d06d8b71876b1512029e66ef25c4abc9c9..0000000000000000000000000000000000000000
--- a/scripts/buildStatistics.js
+++ /dev/null
@@ -1,20 +0,0 @@
-import buildStatistics from './fastaStatsBuilder.js'
-
-/**
- * Wrapper file of the fastaStatsBuilder to compute the
- * statistics from the command line, with the
- * npm script 'npm run stats'.
- */
-buildStatistics().then(result => {
- // Stringify the stats object with a replacer function
- // to handle the sets.
- const stringifiedStats = JSON.stringify(result, (key, value) => {
- return value instanceof Set ? [...value] : value
- }, 2)
-
- console.log(stringifiedStats)
- process.exit(0)
-}).catch(err => {
- console.log(err)
- process.exit(1)
-})
diff --git a/scripts/fastaStatsBuilder.js b/scripts/fastaStatsBuilder.js
deleted file mode 100644
index b1903c741e6df4052f7de49019b8c47ef56ef093..0000000000000000000000000000000000000000
--- a/scripts/fastaStatsBuilder.js
+++ /dev/null
@@ -1,152 +0,0 @@
-import { createReadStream } from 'node:fs'
-import { readdir } from 'node:fs/promises'
-import { dirname, resolve } from 'node:path'
-import { Writable } from 'node:stream'
-import { pipeline } from 'node:stream/promises'
-import { fileURLToPath } from 'node:url'
-import { SplitFastaStream } from './streams/SplitFastaStream.js'
-import { ParseFastaStream } from './streams/ParseFastaStream.js'
-import { SanitizeFastaStream } from './streams/SanitizeFastaStream.js'
-import { BuildAntibodiesStream } from './streams/BuildAntibodiesStream.js'
-
-/**
- * Statistics of the antibodies.
- */
-const stats = {
- antibodies: 0,
- species: new Set(),
- sources: new Set(),
- antibodiesPerSpecies: {},
- antibodiesPerSource: {},
- antibodiesPerHeavySegments: {},
- antibodiesPerLightSegments: {},
- antibodiesOnlyInSource: {},
- antibodiesInMultipleSources: {}
-}
-
-/**
- * Make a unique list of the sources for an antibody.
- * @param {object} antibody - The given antibody
- * @return {Set<string>} The list of sources present in this antibody
- */
-function listSources(antibody) {
- const sources = new Set()
- antibody.heavyChain.headers.forEach(header => { sources.add(header.source) })
- antibody.lightChain.headers.forEach(header => { sources.add(header.source) })
- return sources
-}
-
-/**
- * Make a unique list of the v gene segments for an antibody.
- * @param {object} antibody - The given antibody
- * @return {object} An object with the two lists of heavy and light chain segments.
- */
-function listSegments(antibody) {
- const segments = {
- heavyChain: new Set(),
- lightChain: new Set()
- }
- antibody.heavyChain.headers.forEach(header => { segments.heavyChain.add(header.vGeneSegment) })
- antibody.lightChain.headers.forEach(header => { segments.lightChain.add(header.vGeneSegment) })
- return segments
-}
-
-/**
- * Build the statistics
- */
-class StatisticsStream extends Writable {
- constructor(options) {
- if (!options) options = {};
- options.objectMode = true;
- super(options);
- }
-
- _write(antibody, encoding, done) {
- const species = antibody.species;
- const sources = listSources(antibody);
- const segments = listSegments(antibody);
-
- // Total antibodies
- stats.antibodies += 1;
-
- // Total species
- stats.species.add(antibody.species);
-
- // Total sources
- stats.sources = stats.sources.union(sources);
-
- // Antibodies per species
- stats.antibodiesPerSpecies[species] = stats.antibodiesPerSpecies[species]
- ? stats.antibodiesPerSpecies[species] + 1
- : 1;
-
- // Antibodies per source
- sources.forEach(source => {
- stats.antibodiesPerSource[source] = stats.antibodiesPerSource[source]
- ? stats.antibodiesPerSource[source] + 1
- : 1;
- });
-
- // Antibodies per heavy segments
- segments.heavyChain.forEach(segment => {
- stats.antibodiesPerHeavySegments[segment] = stats.antibodiesPerHeavySegments[segment]
- ? stats.antibodiesPerHeavySegments[segment] + 1
- : 1;
- });
-
- // Antibodies per light segments
- segments.lightChain.forEach(segment => {
- stats.antibodiesPerLightSegments[segment] = stats.antibodiesPerLightSegments[segment]
- ? stats.antibodiesPerLightSegments[segment] + 1
- : 1;
- });
-
- // Antibodies only in one source
- if (sources.size === 1) {
- const source = Array.from(sources)[0];
- stats.antibodiesOnlyInSource[source] = stats.antibodiesOnlyInSource[source]
- ? stats.antibodiesOnlyInSource[source] + 1
- : 1;
- }
-
- // Antibodies in multiple sources
- if (sources.size >= 1) {
- stats.antibodiesInMultipleSources[sources.size] = stats.antibodiesInMultipleSources[sources.size]
- ? stats.antibodiesInMultipleSources[sources.size] + 1
- : 1;
- }
-
- return done();
- }
-}
-
-// =========================================================================
-
-export default async function () {
- const currentPath = dirname(fileURLToPath(import.meta.url))
- const dataFolderPath = resolve(currentPath, '../data')
- const dataFolder = await readdir(dataFolderPath)
- const fastaList = dataFolder.filter(fileName => {
- return fileName.endsWith('.fasta')
- })
-
- for (const fastaFileName of fastaList) {
- const fastaFile = resolve(dataFolderPath, fastaFileName)
- const species = fastaFileName.replace('.fasta', '').replace('_', ' ')
-
- await pipeline(
- createReadStream(fastaFile),
- new SplitFastaStream(),
- new ParseFastaStream(),
- new SanitizeFastaStream(),
- new BuildAntibodiesStream({ species }),
- new StatisticsStream()
- ).catch(err => {
- console.log(`${fastaFile}: \x1B[1;31merror\x1B[0m`)
- console.log(err.message)
- process.exit(1)
- })
- }
-
- return stats
-}
diff --git a/scripts/fastaValidator.js b/scripts/fastaValidator.js
deleted file mode 100644
index 74593f62c60614dbeedb3b4d60f046df7cf2c37b..0000000000000000000000000000000000000000
--- a/scripts/fastaValidator.js
+++ /dev/null
@@ -1,89 +0,0 @@
-import { createReadStream } from 'node:fs'
-import { readdir } from 'node:fs/promises'
-import { dirname, resolve } from 'node:path'
-import { createHash } from 'node:crypto'
-import { Writable } from 'node:stream'
-import { pipeline } from 'node:stream/promises'
-import { fileURLToPath } from 'node:url'
-import { SplitFastaStream } from './streams/SplitFastaStream.js'
-import { ParseFastaStream } from './streams/ParseFastaStream.js'
-
-const fileNameFormat = /^[A-Z][a-z]+_[a-z]+\.fasta$/
-const idFormat = /^[^\s^]+$/
-const subHeaderFormat = /.+;[^\s]+;[^\s]+;[^\s]+$/
-const sequenceFormat = /^[ABCDEFGHIKLMNPQRSTUVWXYZ]+$/
-
-/**
- * Stream for validating fasta entries.
- */
-export class ValidateFastaStream extends Writable {
- constructor(options) {
- if (!options) options = {};
- options.objectMode = true;
- super(options);
-
- this.sequenceHashes = new Set();
- }
-
- _write(fastaObject, encoding, done) {
- const [id, ...headers] = fastaObject.header.split('|||');
- const sequence = fastaObject.sequence;
-
- if (!idFormat.test(id)) {
- return done(new Error(`\x1B[1;31mError with header: ${header} \nID must not contain any space.\x1B[0m`));
- }
-
- for (const subheader of headers) {
- if (!subHeaderFormat.test(subheader)) {
- return done(new Error(`\x1B[1;31mError with subheader: ${subheader} \nThe subheaders must have an id, V gene segment and source at their end, separated by semicolons: header;id;vGeneSegment;source. ID, V gene segment and source must not contain any space.\x1B[0m`));
- }
- }
-
- if (!sequenceFormat.test(sequence)) {
- return done(new Error(`\x1B[1;31mError with sequence: ${sequence} \nSequences must only contain characters among "ABCDEFGHIKLMNPQRSTUVWXYZ".\x1B[0m`));
- }
-
- const hash = createHash('sha256').update(sequence).digest('hex');
-
- // Check the uniqueness of each sequence trough the whole fasta file
- if (this.sequenceHashes.has(hash)) {
- return done(new Error(`\x1B[1;31mDuplication error with sequence: ${sequence} \nThis one already exist in the file.`));
- } else {
- this.sequenceHashes.add(hash);
- }
-
- return done();
- }
-}
-
-// =========================================================================
-
-const currentPath = dirname(fileURLToPath(import.meta.url))
-const dataFolderPath = resolve(currentPath, '../data')
-const dataFolder = await readdir(dataFolderPath)
-const fastaList = dataFolder.filter(fileName => {
- return fileName.endsWith('.fasta')
-})
-
-for (const fastaFileName of fastaList) {
- // Validate that the fasta file name follows the format "Genus_species.fasta".
- if (!fileNameFormat.test(fastaFileName)) {
- console.log(`\x1B[1;31mError with file name: ${fastaFileName} \nFasta file names must follow the format "Genus_species.fasta".\x1B[0m`)
- process.exit(1)
- }
-
- const fastaFile = resolve(dataFolderPath, fastaFileName)
-
- await pipeline(
- createReadStream(fastaFile, { encoding: 'utf-8' }),
- new SplitFastaStream(),
- new ParseFastaStream(),
- new ValidateFastaStream(),
- ).then(async () => {
- console.log(`${fastaFile}: \x1B[1;32mvalidation complete\x1B[0m`)
- }).catch(err => {
- console.log(`${fastaFile}: \x1B[1;31merror\x1B[0m`)
- console.log(err.message)
- process.exit(1)
- })
-}
diff --git a/src/client/components/TheStatisticsPage.vue b/src/client/components/TheStatisticsPage.vue
index 403386fed20b0207b9e68b53116ba3a4e1f3d7af..6aeeed698d40a8f4736d3bce36184ae8bfaeca37 100644
--- a/src/client/components/TheStatisticsPage.vue
+++ b/src/client/components/TheStatisticsPage.vue
@@ -119,8 +119,8 @@ onMounted(() => {
watch(() => statistics.value?.antibodiesPerSpecies, () => buildSpeciesPlot())
watch(() => statistics.value?.antibodiesPerSource, () => buildSourcesPlot())
-watch(() => statistics.value?.antibodiesPerHeavySegments, () => buildHeavySegmentsPlot())
-watch(() => statistics.value?.antibodiesPerLightSegments, () => buildLightSegmentsPlot())
+watch(() => statistics.value?.antibodiesPerHeavySegment, () => buildHeavySegmentsPlot())
+watch(() => statistics.value?.antibodiesPerLightSegment, () => buildLightSegmentsPlot())
watch(() => statistics.value, () => buildSankeyPlot())
@@ -168,9 +168,9 @@ function buildHeavySegmentsPlot() {
data[0].values = []
data[0].labels = []
- const antibodiesPerHeavySegments = Object.entries(statistics.value?.antibodiesPerHeavySegments)
+ const antibodiesPerHeavySegment = Object.entries(statistics.value?.antibodiesPerHeavySegment)
- for (const [source, number] of antibodiesPerHeavySegments) {
+ for (const [source, number] of antibodiesPerHeavySegment) {
data[0].labels.push(`${source} - <i>${number.toLocaleString()}<\i>`)
data[0].values.push(number)
}
@@ -186,9 +186,9 @@ function buildLightSegmentsPlot() {
data[0].values = []
data[0].labels = []
- const antibodiesPerLightSegments = Object.entries(statistics.value?.antibodiesPerLightSegments)
+ const antibodiesPerLightSegment = Object.entries(statistics.value?.antibodiesPerLightSegment)
- for (const [source, number] of antibodiesPerLightSegments) {
+ for (const [source, number] of antibodiesPerLightSegment) {
data[0].labels.push(`${source} - <i>${number.toLocaleString()}<\i>`)
data[0].values.push(number)
}
diff --git a/scripts/buildDatabase.js b/src/scripts/buildDatabase.js
similarity index 90%
rename from scripts/buildDatabase.js
rename to src/scripts/buildDatabase.js
index 8ff878cc3eb02a952d54113d165cdc49e25548ec..c18da80b4e88e3dcfae7f8f163566e362ec5e3bd 100644
--- a/scripts/buildDatabase.js
+++ b/src/scripts/buildDatabase.js
@@ -1,5 +1,5 @@
import buildDatabase from './databaseBuilder.js'
-import config from '../src/server/config/env.js'
+import config from '../server/config/env.js'
console.log(`--- Start building the \x1B[1m${config.ABSD_DB_NAME}\x1B[0m database`)
diff --git a/scripts/databaseBuilder.js b/src/scripts/databaseBuilder.js
similarity index 64%
rename from scripts/databaseBuilder.js
rename to src/scripts/databaseBuilder.js
index e63c2d6342b3c34139b447c847b5962d96042bd6..a13774cb5e7f1244c3dc11fb3195835d0c5ad52f 100644
--- a/scripts/databaseBuilder.js
+++ b/src/scripts/databaseBuilder.js
@@ -1,5 +1,5 @@
import { createReadStream } from 'node:fs'
-import { readdir } from 'node:fs/promises'
+import { readdir, readFile } from 'node:fs/promises'
import { dirname, resolve } from 'node:path'
import { pipeline } from 'node:stream/promises'
import { fileURLToPath } from 'node:url'
@@ -11,9 +11,9 @@ import { BuildAntibodiesStream } from './streams/BuildAntibodiesStream.js'
import { GenerateHashIdStream } from './streams/GenerateHashIdStream.js'
import { GroupAntibodiesStream } from './streams/GroupAntibodiesStream.js'
import { InsertAntibodiesStream } from './streams/InsertAntibodiesStream.js'
-import AntibodySchema from '../src/server/schemas/Antibodies.json' with { type: "json" }
-import StatisticsSchema from '../src/server/schemas/Statistics.json' with { type: "json" }
-import config from '../src/server/config/env.js'
+import AntibodySchema from '../server/schemas/Antibodies.json' with { type: "json" }
+import StatisticsSchema from '../server/schemas/Statistics.json' with { type: "json" }
+import config from '../server/config/env.js'
/**
* Create or cleanup existing database to repopulate it
@@ -53,17 +53,63 @@ async function createDatabase() {
console.log(`Database \x1B[1;32m${config.ABSD_DB_NAME}\x1B[0m created`)
}
+/**
+ * Insert the last statistics file data into the database.
+ * This process is simple enough to not need streams.
+ * @param {object} stats - The statistics object
+ * @param {object} dbConfig - An object with the database configuration
+ * @returns {Promise<object>} - A promise with the results of the insertion.
+ */
+async function insertStatistics(stats, dbConfig) {
+ const uri = `mongodb://${dbConfig.host}:${dbConfig.port}`
+ const mongoClient = new MongoClient(uri)
+ const db = mongoClient.db(dbConfig.name)
+ const collection = db.collection('statistics')
+
+ return collection.insertOne(stats)
+}
+
+/**
+ * Get the last statistics from the stats files.
+ * @returns {Promise<object>} A promise with the statistics object.
+ */
+async function getStatistics() {
+ const currentPath = dirname(fileURLToPath(import.meta.url))
+ const dataFolderPath = resolve(currentPath, '../../data')
+ const dataFolder = await readdir(dataFolderPath)
+
+ const statsFilePath = dataFolder
+ .filter((file) => { return file.endsWith('-stats.json') })
+ .sort()
+ .reverse()
+ .map(file => { return resolve(dataFolderPath, file) })
+ .shift()
+
+ const statsDate = new Date(statsFilePath.match(/(\d{4}-\d{2}-\d{2})-stats/)[1])
+ const statsFile = await readFile(statsFilePath, 'utf8')
+ const stats = JSON.parse(statsFile)
+ stats.versionDate = statsDate
+
+ return stats
+}
+
// =========================================================================
export default async function buildDatabase() {
const currentPath = dirname(fileURLToPath(import.meta.url))
- const dataFolderPath = resolve(currentPath, '../data')
+ const dataFolderPath = resolve(currentPath, '../../data')
const dataFolder = await readdir(dataFolderPath)
const fastaList = dataFolder.filter(fileName => {
return fileName.endsWith('.fasta')
})
+ const stats = await getStatistics()
await createDatabase()
+ await insertStatistics(stats, {
+ host: config.ABSD_DB_HOST,
+ port: config.ABSD_DB_PORT,
+ name: config.ABSD_DB_NAME
+ })
for (const fastaFileName of fastaList) {
const fastaFile = resolve(dataFolderPath, fastaFileName)
diff --git a/src/scripts/displayStatistics.js b/src/scripts/displayStatistics.js
new file mode 100644
index 0000000000000000000000000000000000000000..b851c867782f07d4324a7d34a247c512a428d5e4
--- /dev/null
+++ b/src/scripts/displayStatistics.js
@@ -0,0 +1,13 @@
+import buildStatistics from './fastaStatsBuilder.js'
+
+/**
+ * Wrapper file of the fastaStatsBuilder to display the
+ * statistics from the command line, using a npm script.
+ */
+buildStatistics().then(stats => {
+ console.log(stats.toString())
+ process.exit(0)
+}).catch(err => {
+ console.log(err)
+ process.exit(1)
+})
diff --git a/src/scripts/fastaStatsBuilder.js b/src/scripts/fastaStatsBuilder.js
new file mode 100644
index 0000000000000000000000000000000000000000..873be1644d25bda0de326b6739488f1fc8d98a8f
--- /dev/null
+++ b/src/scripts/fastaStatsBuilder.js
@@ -0,0 +1,44 @@
+import { createReadStream } from 'node:fs'
+import { readdir } from 'node:fs/promises'
+import { dirname, resolve } from 'node:path'
+import { pipeline } from 'node:stream/promises'
+import { fileURLToPath } from 'node:url'
+import { SplitFastaStream } from './streams/SplitFastaStream.js'
+import { ParseFastaStream } from './streams/ParseFastaStream.js'
+import { SanitizeFastaStream } from './streams/SanitizeFastaStream.js'
+import { BuildAntibodiesStream } from './streams/BuildAntibodiesStream.js'
+import { StatisticsStream } from './streams/StatisticsStream.js'
+import { Statistics } from '../server/models/Statistics.js'
+
+// =========================================================================
+
+export default async function () {
+ const currentPath = dirname(fileURLToPath(import.meta.url))
+ const dataFolderPath = resolve(currentPath, '../../data')
+ const dataFolder = await readdir(dataFolderPath)
+ const fastaList = dataFolder.filter(fileName => {
+ return fileName.endsWith('.fasta')
+ })
+
+ const stats = new Statistics()
+
+ for (const fastaFileName of fastaList) {
+ const fastaFile = resolve(dataFolderPath, fastaFileName)
+ const species = fastaFileName.replace('.fasta', '').replace('_', ' ')
+
+ await pipeline(
+ createReadStream(fastaFile),
+ new SplitFastaStream(),
+ new ParseFastaStream(),
+ new SanitizeFastaStream(),
+ new BuildAntibodiesStream({ species }),
+ new StatisticsStream({ stats })
+ ).catch(err => {
+ console.log(`${fastaFile}: \x1B[1;31merror\x1B[0m`)
+ console.log(err.message)
+ process.exit(1)
+ })
+ }
+
+ return stats
+}
diff --git a/src/scripts/fastaValidator.js b/src/scripts/fastaValidator.js
new file mode 100644
index 0000000000000000000000000000000000000000..0dbf374e836df3e9060aeb9f364eeeaf33e474b9
--- /dev/null
+++ b/src/scripts/fastaValidator.js
@@ -0,0 +1,40 @@
+import { createReadStream } from 'node:fs'
+import { readdir } from 'node:fs/promises'
+import { dirname, resolve } from 'node:path'
+import { pipeline } from 'node:stream/promises'
+import { fileURLToPath } from 'node:url'
+import { SplitFastaStream } from './streams/SplitFastaStream.js'
+import { ParseFastaStream } from './streams/ParseFastaStream.js'
+import { ValidateFastaStream } from './streams/ValidateFastaStream.js'
+
+// =========================================================================
+
+const currentPath = dirname(fileURLToPath(import.meta.url))
+const dataFolderPath = resolve(currentPath, '../../data')
+const dataFolder = await readdir(dataFolderPath)
+const fastaList = dataFolder.filter(fileName => {
+ return fileName.endsWith('.fasta')
+})
+
+for (const fastaFileName of fastaList) {
+ // Validate that the fasta file name follows the format "Genus_species.fasta".
+ if (!ValidateFastaStream.fileNameFormat.test(fastaFileName)) {
+ console.log(`\x1B[1;31mError with file name: ${fastaFileName} \nFasta file names must follow the format "Genus_species.fasta".\x1B[0m`)
+ process.exit(1)
+ }
+
+ const fastaFile = resolve(dataFolderPath, fastaFileName)
+
+ await pipeline(
+ createReadStream(fastaFile, { encoding: 'utf-8' }),
+ new SplitFastaStream(),
+ new ParseFastaStream(),
+ new ValidateFastaStream(),
+ ).then(async () => {
+ console.log(`${fastaFile}: \x1B[1;32mvalidation complete\x1B[0m`)
+ }).catch(err => {
+ console.log(`${fastaFile}: \x1B[1;31merror\x1B[0m`)
+ console.log(err.message)
+ process.exit(1)
+ })
+}
diff --git a/scripts/streams/BuildAntibodiesStream.js b/src/scripts/streams/BuildAntibodiesStream.js
similarity index 92%
rename from scripts/streams/BuildAntibodiesStream.js
rename to src/scripts/streams/BuildAntibodiesStream.js
index a52392e47e699028af639adecb2dd1f68d70effc..5461dbf9a173f83cffeca33fa36faae333d54906 100644
--- a/scripts/streams/BuildAntibodiesStream.js
+++ b/src/scripts/streams/BuildAntibodiesStream.js
@@ -54,11 +54,15 @@ export class BuildAntibodiesStream extends Transform {
}
_transform(fastaEntry, encoding, done) {
+ // Light chains always come first, so store it
+ // for the next entry.
if (!this.lightChain) {
this.lightChain = fastaEntry;
return done();
}
+ // If a light chain is stored, then we can build
+ // the antibody.
this.push({
id: this.lightChain.header.split('|||')[0],
species: this.species,
diff --git a/scripts/streams/GenerateHashIdStream.js b/src/scripts/streams/GenerateHashIdStream.js
similarity index 62%
rename from scripts/streams/GenerateHashIdStream.js
rename to src/scripts/streams/GenerateHashIdStream.js
index 5221b835f956b37ea9be278d7dfe364ef198b718..2a70434f0d95a81fcd094f93811f5565524f4b51 100644
--- a/scripts/streams/GenerateHashIdStream.js
+++ b/src/scripts/streams/GenerateHashIdStream.js
@@ -1,5 +1,5 @@
-import { createHash } from "crypto";
import { Transform } from "stream";
+import { Antibody } from "../../server/models/Antibody.js";
/**
* Add the hashId field to antibodies object.
@@ -13,14 +13,7 @@ export class GenerateHashIdStream extends Transform {
}
_transform(antibody, encoding, done) {
- const hashInput = antibody.species +
- antibody.heavyChain.sequence +
- antibody.lightChain.sequence;
-
- antibody.hashId = createHash('sha256')
- .update(hashInput, 'ascii')
- .digest('hex');
-
+ antibody.hashId = Antibody.generateHashId(antibody)
this.push(antibody);
return done();
}
diff --git a/scripts/streams/GroupAntibodiesStream.js b/src/scripts/streams/GroupAntibodiesStream.js
similarity index 100%
rename from scripts/streams/GroupAntibodiesStream.js
rename to src/scripts/streams/GroupAntibodiesStream.js
diff --git a/scripts/streams/InsertAntibodiesStream.js b/src/scripts/streams/InsertAntibodiesStream.js
similarity index 96%
rename from scripts/streams/InsertAntibodiesStream.js
rename to src/scripts/streams/InsertAntibodiesStream.js
index f92129b726812852f51bb1593955c7df6044ca5c..9ed83b21810bc5362bcea3a6b34187d5b8136a76 100644
--- a/scripts/streams/InsertAntibodiesStream.js
+++ b/src/scripts/streams/InsertAntibodiesStream.js
@@ -1,6 +1,6 @@
import { MongoClient } from "mongodb";
import { Writable } from "stream";
-import config from "../../src/server/config/env.js";
+import config from "../../server/config/env.js";
/**
* Insert groups of antibodies into the MongoDB database.
diff --git a/scripts/streams/ParseFastaStream.js b/src/scripts/streams/ParseFastaStream.js
similarity index 100%
rename from scripts/streams/ParseFastaStream.js
rename to src/scripts/streams/ParseFastaStream.js
diff --git a/scripts/streams/SanitizeFastaStream.js b/src/scripts/streams/SanitizeFastaStream.js
similarity index 100%
rename from scripts/streams/SanitizeFastaStream.js
rename to src/scripts/streams/SanitizeFastaStream.js
diff --git a/scripts/streams/SplitFastaStream.js b/src/scripts/streams/SplitFastaStream.js
similarity index 100%
rename from scripts/streams/SplitFastaStream.js
rename to src/scripts/streams/SplitFastaStream.js
diff --git a/src/scripts/streams/StatisticsStream.js b/src/scripts/streams/StatisticsStream.js
new file mode 100644
index 0000000000000000000000000000000000000000..1a68970db2470509a79d804b33f19f7d6e7dcda0
--- /dev/null
+++ b/src/scripts/streams/StatisticsStream.js
@@ -0,0 +1,75 @@
+import { Writable } from 'node:stream'
+import { Antibody } from '../../server/models/Antibody.js'
+
+// =========================================================================
+
+/**
+ * Build the statistics by incrementing a given stats object.
+ */
+export class StatisticsStream extends Writable {
+ constructor(options) {
+ if (!options) options = {};
+ options.objectMode = true;
+ super(options);
+
+ this.stats = options.stats
+ }
+
+ _write(antibody, encoding, done) {
+ const species = antibody.species;
+ const sources = Antibody.listSources(antibody);
+ const segments = Antibody.listSegments(antibody);
+
+ // Total antibodies
+ this.stats.antibodies += 1;
+
+ // Total species
+ this.stats.species.add(antibody.species);
+
+ // Total sources
+ this.stats.sources = this.stats.sources.union(sources);
+
+ // Antibodies per species
+ this.stats.antibodiesPerSpecies[species] = this.stats.antibodiesPerSpecies[species]
+ ? this.stats.antibodiesPerSpecies[species] + 1
+ : 1;
+
+ // Antibodies per source
+ sources.forEach(source => {
+ this.stats.antibodiesPerSource[source] = this.stats.antibodiesPerSource[source]
+ ? this.stats.antibodiesPerSource[source] + 1
+ : 1;
+ });
+
+ // Antibodies per heavy segment
+ segments.heavyChain.forEach(segment => {
+ this.stats.antibodiesPerHeavySegment[segment] = this.stats.antibodiesPerHeavySegment[segment]
+ ? this.stats.antibodiesPerHeavySegment[segment] + 1
+ : 1;
+ });
+
+ // Antibodies per light segment
+ segments.lightChain.forEach(segment => {
+ this.stats.antibodiesPerLightSegment[segment] = this.stats.antibodiesPerLightSegment[segment]
+ ? this.stats.antibodiesPerLightSegment[segment] + 1
+ : 1;
+ });
+
+ // Antibodies only in one source
+ if (sources.size === 1) {
+ const source = Array.from(sources)[0];
+ this.stats.antibodiesOnlyInSource[source] = this.stats.antibodiesOnlyInSource[source]
+ ? this.stats.antibodiesOnlyInSource[source] + 1
+ : 1;
+ }
+
+ // Antibodies in multiple sources
+ if (sources.size >= 1) {
+ this.stats.antibodiesInMultipleSources[sources.size] = this.stats.antibodiesInMultipleSources[sources.size]
+ ? this.stats.antibodiesInMultipleSources[sources.size] + 1
+ : 1;
+ }
+
+ return done();
+ }
+}
diff --git a/src/scripts/streams/ValidateFastaStream.js b/src/scripts/streams/ValidateFastaStream.js
new file mode 100644
index 0000000000000000000000000000000000000000..246364da6dc5e4c1be6443ccd73e9509d48c83bb
--- /dev/null
+++ b/src/scripts/streams/ValidateFastaStream.js
@@ -0,0 +1,50 @@
+import { createHash } from 'crypto';
+import { Writable } from 'stream';
+
+/**
+ * Stream for validating fasta entries.
+ */
+export class ValidateFastaStream extends Writable {
+ static fileNameFormat = /^[A-Z][a-z]+_[a-z]+\.fasta$/
+ static idFormat = /^[^\s^]+$/
+ static subHeaderFormat = /.+;[^\s]+;[^\s]+;[^\s]+$/
+ static sequenceFormat = /^[ABCDEFGHIKLMNPQRSTUVWXYZ]+$/
+
+ constructor(options) {
+ if (!options) options = {};
+ options.objectMode = true;
+ super(options);
+
+ this.sequenceHashes = new Set();
+ }
+
+ _write(fastaObject, encoding, done) {
+ const [id, ...headers] = fastaObject.header.split('|||');
+ const sequence = fastaObject.sequence;
+
+ if (!ValidateFastaStream.idFormat.test(id)) {
+ return done(new Error(`\x1B[1;31mError with header: ${header} \nID must not contain any space.\x1B[0m`));
+ }
+
+ for (const subheader of headers) {
+ if (!ValidateFastaStream.subHeaderFormat.test(subheader)) {
+ return done(new Error(`\x1B[1;31mError with subheader: ${subheader} \nThe subheaders must have an id, V gene segment and source at their end, separated by semicolons: header;id;vGeneSegment;source. ID, V gene segment and source must not contain any space.\x1B[0m`));
+ }
+ }
+
+ if (!ValidateFastaStream.sequenceFormat.test(sequence)) {
+ return done(new Error(`\x1B[1;31mError with sequence: ${sequence} \nSequences must only contain characters among "ABCDEFGHIKLMNPQRSTUVWXYZ".\x1B[0m`));
+ }
+
+ const hash = createHash('sha256').update(sequence).digest('hex');
+
+ // Check the uniqueness of each sequence trough the whole fasta file
+ if (this.sequenceHashes.has(hash)) {
+ return done(new Error(`\x1B[1;31mDuplication error with sequence: ${sequence} \nThis one already exist in the file.`));
+ } else {
+ this.sequenceHashes.add(hash);
+ }
+
+ return done();
+ }
+}
diff --git a/src/server/app.js b/src/server/app.js
index 9891fbbb8af75b16ca42aea91758beafcf6e2383..a635b5ab67400fc56d785b0c4643c49d5cbc0056 100644
--- a/src/server/app.js
+++ b/src/server/app.js
@@ -20,7 +20,7 @@ import { fileURLToPath } from 'node:url'
import fastifyMongo from '@fastify/mongodb'
import fastifyStatic from '@fastify/static'
import Fastify from 'fastify'
-import buildDatabase from "../../scripts/databaseBuilder.js"
+import buildDatabase from "../../src/scripts/databaseBuilder.js"
import envConfig from './config/env.js'
import { ArchiveJobs } from './models/ArchiveJobs.js'
import antibodiesCountRoute from './routes/antibodiesCountRoute.js'
@@ -37,6 +37,7 @@ import downloadsRoute from './routes/downloadsRoute.js'
import healthCheckRoute from './routes/healthCheckRoute.js'
import readyCheckRoute from './routes/readyCheckRoute.js'
import statisticsRoute from './routes/statisticsRoute.js'
+import databaseIsSync from './utils/databaseIsSync.js'
/**
* Setup the fastify instance with custom
@@ -164,7 +165,9 @@ fastify.listen({
host: envConfig.ABSD_SERVER_HOST,
port: envConfig.ABSD_SERVER_PORT
}).then(async () => {
- if (envConfig.NODE_ENV === 'production') {
+ const dbShouldBeRebuilt = !await databaseIsSync(fastify)
+
+ if (envConfig.NODE_ENV === 'production' && dbShouldBeRebuilt) {
return await buildDatabase()
}
}).then((dbResults) => {
diff --git a/src/server/models/Antibody.js b/src/server/models/Antibody.js
new file mode 100644
index 0000000000000000000000000000000000000000..8c8e67b869f63ed729d58197335f813ca7f9e581
--- /dev/null
+++ b/src/server/models/Antibody.js
@@ -0,0 +1,90 @@
+// 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 { createHash } from "node:crypto";
+
+/**
+ * The main Antibody model.
+ * Purely static class to factorize the Antibody related functions.
+ */
+export class Antibody {
+ /**
+ * Make a unique list of the sources for an antibody.
+ * @param {object} antibody - The given antibody
+ * @return {Set<string>} The list of sources present in this antibody
+ */
+ static listSources(antibody) {
+ const sources = new Set()
+ antibody.heavyChain.headers.forEach(header => { sources.add(header.source) })
+ antibody.lightChain.headers.forEach(header => { sources.add(header.source) })
+ return sources
+ }
+
+ /**
+ * Make a unique list of the v gene segments for an antibody.
+ * @param {object} antibody - The given antibody
+ * @return {object} An object with the two lists of heavy and light chain segments.
+ */
+ static listSegments(antibody) {
+ const segments = {
+ heavyChain: new Set(),
+ lightChain: new Set()
+ }
+ antibody.heavyChain.headers.forEach(header => { segments.heavyChain.add(header.vGeneSegment) })
+ antibody.lightChain.headers.forEach(header => { segments.lightChain.add(header.vGeneSegment) })
+ return segments
+ }
+
+ /**
+ * Generate a sha256 hash for a given antibody,
+ * using the species, light and heavy sequences.
+ * @param {object} antibody - The given antibody
+ * @returns {string} The sha256 hash
+ */
+ static generateHashId(antibody) {
+ const hashInput = antibody.species +
+ antibody.heavyChain.sequence +
+ antibody.lightChain.sequence;
+
+ return createHash('sha256')
+ .update(hashInput, 'ascii')
+ .digest('hex');
+ }
+
+ /**
+ * Turn an antibody object into a FASTA entry,
+ * using the rawFasta property.
+ * @param {object} antibody - The given antibody
+ * @returns {string} The antibody as a FASTA data string
+ */
+ static toFasta(antibody) {
+ return [
+ `>${antibody.lightChain.rawFasta}`,
+ antibody.lightChain.sequence,
+ `>${antibody.heavyChain.rawFasta}`,
+ antibody.heavyChain.sequence
+ ].join('\n')
+ }
+
+ /**
+ * Turn an antibody object into string.
+ * @param {object} antibody - The given antibody
+ * @returns {string} the stringified antibody
+ */
+ static toString(antibody) {
+ return JSON.stringify(antibody)
+ }
+}
diff --git a/src/server/models/AntibodyFastaStream.js b/src/server/models/AntibodyFastaStream.js
index bc68171921d1402e4786a90e5a16710dd8f88784..2e1f61a707868267b91df05e2f84252a6cb289b7 100644
--- a/src/server/models/AntibodyFastaStream.js
+++ b/src/server/models/AntibodyFastaStream.js
@@ -15,7 +15,7 @@
// along with this program. If not, see <http://www.gnu.org/licenses/>.
import { Transform } from "node:stream"
-import antibodyToFasta from "../utils/antibodyToFasta.js"
+import { Antibody } from "./Antibody.js"
/**
* Transform stream for turning antibodies entries from the database
@@ -31,10 +31,10 @@ export default class AntibodyFastaStream extends Transform {
super(options)
}
- // Use the antibodyToFasta function to simply turn an entry into
+ // Use the toFasta function to simply turn an entry into
// a FASTA string.
_transform(antibody, encoding, done) {
- this.push(`${antibodyToFasta(antibody)}\n`)
+ this.push(`${Antibody.toFasta(antibody)}\n`)
return done()
}
}
diff --git a/src/server/models/AntibodyJsonStream.js b/src/server/models/AntibodyJsonStream.js
index 424b579b0a44158270ea77034bb2efa3a8f7b164..72f55865b26dd744dc1c8e31c451c2f8df38eef7 100644
--- a/src/server/models/AntibodyJsonStream.js
+++ b/src/server/models/AntibodyJsonStream.js
@@ -15,6 +15,7 @@
// along with this program. If not, see <http://www.gnu.org/licenses/>.
import { Transform } from "node:stream"
+import { Antibody } from "./Antibody.js"
/**
* Transform stream for turning antibodies entries from the database
@@ -51,12 +52,12 @@ export default class AntibodyJsonStream extends Transform {
// will be the last one.
_transform(antibody, encoding, done) {
if (this.firstEntry) {
- this.push(JSON.stringify(antibody))
+ this.push(Antibody.toString(antibody))
this.firstEntry = false
return done()
}
- this.push(`,\n${JSON.stringify(antibody)}`)
+ this.push(`,\n${Antibody.toString(antibody)}`)
return done()
}
diff --git a/src/server/utils/antibodyToFasta.js b/src/server/models/Statistics.js
similarity index 54%
rename from src/server/utils/antibodyToFasta.js
rename to src/server/models/Statistics.js
index 56812e21d1e49e32e0d29b88ff0a26d04c228ff6..d38b5122266020350fe70af4b80ce3b7699c3376 100644
--- a/src/server/utils/antibodyToFasta.js
+++ b/src/server/models/Statistics.js
@@ -15,16 +15,27 @@
// along with this program. If not, see <http://www.gnu.org/licenses/>.
/**
- * Turn an antibody object into a FASTA entry,
- * using the rawFasta property.
- * @param {object} antibody - The antibody from the database
- * @returns {string} The antibody as a FASTA data string
+ * Statistics about the antibodies.
*/
-export default function antibodyToFasta(antibody) {
- return [
- `>${antibody.lightChain.rawFasta}`,
- antibody.lightChain.sequence,
- `>${antibody.heavyChain.rawFasta}`,
- antibody.heavyChain.sequence
- ].join('\n')
+export class Statistics {
+ antibodies = 0
+ species = new Set()
+ sources = new Set()
+ antibodiesPerSpecies = {}
+ antibodiesPerSource = {}
+ antibodiesPerHeavySegment = {}
+ antibodiesPerLightSegment = {}
+ antibodiesOnlyInSource = {}
+ antibodiesInMultipleSources = {}
+
+ /**
+ * Stringify the stats object with a replacer function
+ * to handle the sets.
+ * @returns {string} The stringified stats object
+ */
+ toString() {
+ return JSON.stringify(this, (key, value) => {
+ return value instanceof Set ? [...value] : value
+ }, 2)
+ }
}
diff --git a/src/server/routes/antibodiesDownloadRoute.js b/src/server/routes/antibodiesDownloadRoute.js
index 8fbf2587337ba9ff1e92bba17376b003c57631d3..5b2b933695b02b4acbc0b931987faa593b2842dc 100644
--- a/src/server/routes/antibodiesDownloadRoute.js
+++ b/src/server/routes/antibodiesDownloadRoute.js
@@ -58,12 +58,15 @@ export default {
],
handler: function (request, reply) {
const archiveId = `absd-${randomUUID()}`
+ const requestFields = request.query.format === 'fasta'
+ ? fieldsProjection.fasta
+ : fieldsProjection.json
this.archiveJobs.add(new ArchiveBuilder({
archiveId,
archiveFormat: request.query.format,
requestWhere: request.where,
- requestFields: fieldsProjection
+ requestFields
}))
reply.code(202).send({
diff --git a/src/server/routes/readyCheckRoute.js b/src/server/routes/readyCheckRoute.js
index 5f45c42b12621bd4f0a706b8a526cfe5a54d9663..2ec8df6c46b393ef58917fe78b819191a7955d28 100644
--- a/src/server/routes/readyCheckRoute.js
+++ b/src/server/routes/readyCheckRoute.js
@@ -22,6 +22,7 @@
export default {
method: 'GET',
url: '/ready',
+ logLevel: 'warn',
handler: function (request, reply) {
if (this.serverIsReady) {
return reply
diff --git a/src/server/routes/statisticsRoute.js b/src/server/routes/statisticsRoute.js
index b175351cebf056b8e9b9bcfdb8db1554b1d7d215..eb033bcdf0944c0bd496d6f75df5e54b1989d0a1 100644
--- a/src/server/routes/statisticsRoute.js
+++ b/src/server/routes/statisticsRoute.js
@@ -14,15 +14,6 @@
// 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 { readFileSync, readdirSync } from 'node:fs'
-import { dirname, resolve } from 'node:path'
-import { fileURLToPath } from 'node:url'
-
-/**
- * The absolute path of this file.
- */
-const currentPath = dirname(fileURLToPath(import.meta.url))
-
/**
* Route for getting the statistics data.
*/
@@ -30,23 +21,16 @@ export default {
method: 'GET',
url: '/api/statistics',
handler: function (request, reply) {
- const dirPath = resolve(currentPath, '../../../data')
- const statisticsList = readdirSync(dirPath)
- .filter((file) => {
- return file.endsWith('-stats.json')
+ this.mongo.db
+ .collection('statistics')
+ .findOne()
+ .then(stats => {
+ return reply
+ .code(200)
+ .header('content-type', 'application/json')
+ .send(stats)
+ }).catch(err => {
+ reply.code(500).send(err)
})
- .sort()
- .reverse()
- .map(file => {
- return resolve(dirPath, file)
- })
- .map(path => {
- return readFileSync(path, 'utf-8')
- })
- .map(fileContent => {
- return JSON.parse(fileContent)
- })
-
- reply.send(statisticsList[0])
}
}
diff --git a/src/server/schemas/Statistics.json b/src/server/schemas/Statistics.json
index d9e220a9965640df974b3be65fc30da4ce21b1a0..2c53ea243ee4b4055ce81365dde750859c0d1873 100644
--- a/src/server/schemas/Statistics.json
+++ b/src/server/schemas/Statistics.json
@@ -6,17 +6,29 @@
"_id": {
"bsonType": "objectId"
},
+ "versionDate": {
+ "description": "Date of this database version",
+ "bsonType": "date"
+ },
"antibodies": {
"description": "Total number of antibodies.",
"bsonType": "int"
},
"species": {
- "description": "Total number of species.",
- "bsonType": "int"
+ "description": "List of species.",
+ "bsonType": "array",
+ "items": {
+ "bsonType": "string",
+ "pattern": "^[A-Z][a-z]+\\s[a-z]+$"
+ }
},
"sources": {
- "description": "Total number of sources.",
- "bsonType": "int"
+ "description": "List of sources.",
+ "bsonType": "array",
+ "items": {
+ "bsonType": "string",
+ "pattern": "^.+$"
+ }
},
"antibodiesPerSpecies": {
"description": "Total number of antibodies per species. Keys must follow the species name pattern.",
@@ -36,6 +48,24 @@
}
}
},
+ "antibodiesPerHeavySegment": {
+ "description": "Total number of antibodies per heavy segment.",
+ "bsonType": "object",
+ "patternProperties": {
+ "^IGHV[0-9]+$": {
+ "bsonType": "int"
+ }
+ }
+ },
+ "antibodiesPerLightSegment": {
+ "description": "Total number of antibodies per light segment.",
+ "bsonType": "object",
+ "patternProperties": {
+ "^IG[LK]V[0-9]+$": {
+ "bsonType": "int"
+ }
+ }
+ },
"antibodiesOnlyInSource": {
"description": "Total number of antibodies that are unique for a given source and thus not repeated elsewhere.",
"bsonType": "object",
diff --git a/src/server/utils/archiveBuilderWorker.js b/src/server/utils/archiveBuilderWorker.js
index 68fed5cd0357dadbbb8e72c228f94c4b76627417..a13de23a6abbe5868686b45c24d69ce2a5994931 100644
--- a/src/server/utils/archiveBuilderWorker.js
+++ b/src/server/utils/archiveBuilderWorker.js
@@ -1,3 +1,19 @@
+// 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 { createReadStream, createWriteStream } from "node:fs"
import { rm } from "node:fs/promises"
import { tmpdir } from "node:os"
@@ -17,22 +33,17 @@ const dataFormat = workerData.archiveFormat
const tmpFileExt = dataFormat === 'fasta' ? '.fasta' : '.json'
const tmpFileName = `${workerData.archiveId}${tmpFileExt}`
const tmpFilePath = join(tmpDir, tmpFileName)
-
const archiveName = `${tmpFileName}.gz`
const archivePath = join(tmpDir, archiveName)
-// TO DO: this should not be handled there but in the route,
-// before the ArchiveBuilder intialisation
-const projection = dataFormat === 'fasta'
- ? workerData.requestFields.fasta
- : workerData.requestFields.json
-
const mongoURI = `mongodb://${envConfig.ABSD_DB_HOST}:${envConfig.ABSD_DB_PORT}/${envConfig.ABSD_DB_NAME}`
const database = await MongoClient.connect(mongoURI)
const dataStream = database
.db()
.collection('antibodies')
- .find(workerData.requestWhere, { projection })
+ .find(workerData.requestWhere, {
+ projection: workerData.requestFields
+ })
.stream()
const transformStream = dataFormat === 'fasta'
diff --git a/src/server/utils/databaseIsSync.js b/src/server/utils/databaseIsSync.js
new file mode 100644
index 0000000000000000000000000000000000000000..fbeaacf1f0ea23d2ea6f18ca859642ec989ae9ff
--- /dev/null
+++ b/src/server/utils/databaseIsSync.js
@@ -0,0 +1,52 @@
+// 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 { readdir } from 'node:fs/promises'
+import { dirname, resolve } from 'node:path'
+import { fileURLToPath } from 'node:url'
+
+/**
+ * Check if the database is already there and synchronized with the
+ * last version of the data by checking the stats version date.
+ * Used mainly to check if the database should be rebuilt or not.
+ * @param {object} fastify - The Fastify server object
+ * @returns {boolean} If the database is sync or not
+ */
+export default async function databaseIsSync(fastify) {
+ // Get the stats of the current database
+ const dbStats = await fastify.mongo.db
+ .collection('statistics')
+ .findOne()
+
+ // Stop here if the database does not exist
+ if (!dbStats?.versionDate) return false
+
+ // Then fetch the stats of the last stats file for comparison
+ const currentPath = dirname(fileURLToPath(import.meta.url))
+ const dataFolderPath = resolve(currentPath, '../../../data')
+ const dataFolder = await readdir(dataFolderPath)
+
+ const statsFilePath = dataFolder
+ .filter((file) => { return file.endsWith('-stats.json') })
+ .sort()
+ .reverse()
+ .map(file => { return resolve(dataFolderPath, file) })
+ .shift()
+
+ const lastStatsDate = new Date(statsFilePath.match(/(\d{4}-\d{2}-\d{2})-stats/)[1])
+
+ return dbStats.versionDate.getTime() === lastStatsDate.getTime()
+}