From 7e9df72e722e77017f2ef47b8c3765d70d90669a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 26 Mar 2024 09:21:03 +0000 Subject: [PATCH 01/10] chore(deps-dev): bump the minorandpatch group in /website with 4 updates Bumps the minorandpatch group in /website with 4 updates: [@types/react](https://github.com/DefinitelyTyped/DefinitelyTyped/tree/HEAD/types/react), [@typescript-eslint/eslint-plugin](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/eslint-plugin), [@typescript-eslint/parser](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/parser) and [msw](https://github.com/mswjs/msw). Updates `@types/react` from 18.2.70 to 18.2.71 - [Release notes](https://github.com/DefinitelyTyped/DefinitelyTyped/releases) - [Commits](https://github.com/DefinitelyTyped/DefinitelyTyped/commits/HEAD/types/react) Updates `@typescript-eslint/eslint-plugin` from 7.3.1 to 7.4.0 - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/eslint-plugin/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v7.4.0/packages/eslint-plugin) Updates `@typescript-eslint/parser` from 7.3.1 to 7.4.0 - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/parser/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v7.4.0/packages/parser) Updates `msw` from 2.2.10 to 2.2.11 - [Release notes](https://github.com/mswjs/msw/releases) - [Changelog](https://github.com/mswjs/msw/blob/main/CHANGELOG.md) - [Commits](https://github.com/mswjs/msw/compare/v2.2.10...v2.2.11) --- updated-dependencies: - dependency-name: "@types/react" dependency-type: direct:development update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: "@typescript-eslint/eslint-plugin" dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@typescript-eslint/parser" dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: msw dependency-type: direct:development update-type: version-update:semver-patch dependency-group: minorandpatch ... Signed-off-by: dependabot[bot] --- website/package-lock.json | 186 +++++++++++++++++++------------------- website/package.json | 8 +- 2 files changed, 97 insertions(+), 97 deletions(-) diff --git a/website/package-lock.json b/website/package-lock.json index 39c7837171..2b1b2cf5d5 100644 --- a/website/package-lock.json +++ b/website/package-lock.json @@ -57,11 +57,11 @@ "@types/lodash": "^4.17.0", "@types/luxon": "^3.4.2", "@types/node": "^20.11.30", - "@types/react": "^18.2.70", + "@types/react": "^18.2.71", "@types/react-dom": "^18.2.22", "@types/uuid": "^9.0.8", - "@typescript-eslint/eslint-plugin": "^7.3.1", - "@typescript-eslint/parser": "^7.3.1", + "@typescript-eslint/eslint-plugin": "^7.4.0", + "@typescript-eslint/parser": "^7.4.0", "@vitejs/plugin-react": "^4.2.1", "cross-env": "^7.0.3", "daisyui": "^4.8.0", @@ -73,7 +73,7 @@ "eslint-plugin-react": "^7.34.1", "eslint-plugin-react-hooks": "^4.6.0", "jsdom": "^24.0.0", - "msw": "^2.2.10", + "msw": "^2.2.11", "prettier": "3.2.5", "prettier-plugin-astro": "^0.13.0", "sass": "^1.72.0", @@ -3379,9 +3379,9 @@ "integrity": "sha512-hKormJbkJqzQGhziax5PItDUTMAM9uE2XXQmM37dyd4hVM+5aVl7oVxMVUiVQn2oCQFN/LKCZdvSM0pFRqbSmQ==" }, "node_modules/@types/react": { - 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"@typescript-eslint/eslint-plugin": "^7.3.1", - "@typescript-eslint/parser": "^7.3.1", + "@typescript-eslint/eslint-plugin": "^7.4.0", + "@typescript-eslint/parser": "^7.4.0", "@vitejs/plugin-react": "^4.2.1", "cross-env": "^7.0.3", "daisyui": "^4.8.0", @@ -83,7 +83,7 @@ "eslint-plugin-react": "^7.34.1", "eslint-plugin-react-hooks": "^4.6.0", "jsdom": "^24.0.0", - "msw": "^2.2.10", + "msw": "^2.2.11", "prettier": "3.2.5", "prettier-plugin-astro": "^0.13.0", "sass": "^1.72.0", From c7c8ff60c0eb70f3c87af01e3c5a498535728a27 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 26 Mar 2024 17:11:36 +0100 Subject: [PATCH 02/10] chore(deps): bump express from 4.18.3 to 4.19.2 in /keycloak/keycloakify (#1483) Bumps [express](https://github.com/expressjs/express) from 4.18.3 to 4.19.2. - [Release notes](https://github.com/expressjs/express/releases) - [Changelog](https://github.com/expressjs/express/blob/master/History.md) - [Commits](https://github.com/expressjs/express/compare/4.18.3...4.19.2) --- updated-dependencies: - dependency-name: express dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- keycloak/keycloakify/yarn.lock | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/keycloak/keycloakify/yarn.lock b/keycloak/keycloakify/yarn.lock index 94c5623610..6a87c7e63c 100644 --- a/keycloak/keycloakify/yarn.lock +++ b/keycloak/keycloakify/yarn.lock @@ -5790,10 +5790,10 @@ cookie-signature@1.0.6: resolved "https://registry.yarnpkg.com/cookie-signature/-/cookie-signature-1.0.6.tgz#e303a882b342cc3ee8ca513a79999734dab3ae2c" integrity sha512-QADzlaHc8icV8I7vbaJXJwod9HWYp8uCqf1xa4OfNu1T7JVxQIrUgOWtHdNDtPiywmFbiS12VjotIXLrKM3orQ== -cookie@0.5.0: - version "0.5.0" - resolved "https://registry.yarnpkg.com/cookie/-/cookie-0.5.0.tgz#d1f5d71adec6558c58f389987c366aa47e994f8b" - integrity sha512-YZ3GUyn/o8gfKJlnlX7g7xq4gyO6OSuhGPKaaGssGB2qgDUS0gPgtTvoyZLTt9Ab6dC4hfc9dV5arkvc/OCmrw== +cookie@0.6.0: + version "0.6.0" + resolved "https://registry.yarnpkg.com/cookie/-/cookie-0.6.0.tgz#2798b04b071b0ecbff0dbb62a505a8efa4e19051" + integrity sha512-U71cyTamuh1CRNCfpGY6to28lxvNwPG4Guz/EVjgf3Jmzv0vlDp1atT9eS5dDjMYHucpHbWns6Lwf3BKz6svdw== copy-concurrently@^1.0.0: version "1.0.5" @@ -7343,16 +7343,16 @@ expect@^27.5.1: jest-message-util "^27.5.1" express@^4.17.1, express@^4.17.3: - version "4.18.3" - resolved "https://registry.yarnpkg.com/express/-/express-4.18.3.tgz#6870746f3ff904dee1819b82e4b51509afffb0d4" - integrity sha512-6VyCijWQ+9O7WuVMTRBTl+cjNNIzD5cY5mQ1WM8r/LEkI2u8EYpOotESNwzNlyCn3g+dmjKYI6BmNneSr/FSRw== + version "4.19.2" + resolved "https://registry.yarnpkg.com/express/-/express-4.19.2.tgz#e25437827a3aa7f2a827bc8171bbbb664a356465" + integrity sha512-5T6nhjsT+EOMzuck8JjBHARTHfMht0POzlA60WV2pMD3gyXw2LZnZ+ueGdNxG+0calOJcWKbpFcuzLZ91YWq9Q== dependencies: accepts "~1.3.8" array-flatten "1.1.1" body-parser "1.20.2" content-disposition "0.5.4" content-type "~1.0.4" - cookie "0.5.0" + cookie "0.6.0" cookie-signature "1.0.6" debug "2.6.9" depd "2.0.0" From 68bcdaa2572bad8855552ed3429c3237c7fe0e82 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 26 Mar 2024 17:12:07 +0100 Subject: [PATCH 03/10] chore(deps): bump the minorandpatch group in /docs with 5 updates (#1480) Bumps the minorandpatch group in /docs with 5 updates: | Package | From | To | | --- | --- | --- | | [@astrojs/check](https://github.com/withastro/language-tools/tree/HEAD/packages/astro-check) | `0.5.9` | `0.5.10` | | [@astrojs/starlight](https://github.com/withastro/starlight/tree/HEAD/packages/starlight) | `0.21.1` | `0.21.2` | | [astro](https://github.com/withastro/astro/tree/HEAD/packages/astro) | `4.5.6` | `4.5.9` | | [sharp](https://github.com/lovell/sharp) | `0.33.2` | `0.33.3` | | [typescript](https://github.com/Microsoft/TypeScript) | `5.4.2` | `5.4.3` | Updates `@astrojs/check` from 0.5.9 to 0.5.10 - [Release notes](https://github.com/withastro/language-tools/releases) - [Changelog](https://github.com/withastro/language-tools/blob/main/packages/astro-check/CHANGELOG.md) - [Commits](https://github.com/withastro/language-tools/commits/@astrojs/check@0.5.10/packages/astro-check) Updates `@astrojs/starlight` from 0.21.1 to 0.21.2 - [Release notes](https://github.com/withastro/starlight/releases) - [Changelog](https://github.com/withastro/starlight/blob/main/packages/starlight/CHANGELOG.md) - [Commits](https://github.com/withastro/starlight/commits/@astrojs/starlight@0.21.2/packages/starlight) Updates `astro` from 4.5.6 to 4.5.9 - [Release notes](https://github.com/withastro/astro/releases) - [Changelog](https://github.com/withastro/astro/blob/main/packages/astro/CHANGELOG.md) - [Commits](https://github.com/withastro/astro/commits/astro@4.5.9/packages/astro) Updates `sharp` from 0.33.2 to 0.33.3 - [Release notes](https://github.com/lovell/sharp/releases) - [Changelog](https://github.com/lovell/sharp/blob/main/docs/changelog.md) - [Commits](https://github.com/lovell/sharp/compare/v0.33.2...v0.33.3) Updates `typescript` from 5.4.2 to 5.4.3 - [Release notes](https://github.com/Microsoft/TypeScript/releases) - [Changelog](https://github.com/microsoft/TypeScript/blob/main/azure-pipelines.release.yml) - [Commits](https://github.com/Microsoft/TypeScript/compare/v5.4.2...v5.4.3) --- updated-dependencies: - dependency-name: "@astrojs/check" dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: "@astrojs/starlight" dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: astro dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: sharp dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: typescript dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- docs/package-lock.json | 904 +++++++++++++++++++++-------------------- docs/package.json | 10 +- 2 files changed, 458 insertions(+), 456 deletions(-) diff --git a/docs/package-lock.json b/docs/package-lock.json index 1b3401cd97..8bdb07dea6 100644 --- a/docs/package-lock.json +++ b/docs/package-lock.json @@ -8,11 +8,11 @@ "name": "docs2", "version": "0.0.1", "dependencies": { - "@astrojs/check": "^0.5.9", - "@astrojs/starlight": "^0.21.1", - "astro": "^4.5.6", - "sharp": "^0.33.2", - "typescript": "^5.4.2" + "@astrojs/check": "^0.5.10", + "@astrojs/starlight": "^0.21.2", + "astro": "^4.5.9", + "sharp": "^0.33.3", + "typescript": "^5.4.3" } }, "node_modules/@ampproject/remapping": { @@ -28,11 +28,11 @@ } }, "node_modules/@astrojs/check": { - "version": "0.5.9", - "resolved": "https://registry.npmjs.org/@astrojs/check/-/check-0.5.9.tgz", - "integrity": "sha512-+QsQMtYq4oso+gmilJC9HLmdi0glZ+04V/VyyTTPry7n21jqjX9SfgDpLGxMk5cwPC/vwZMkn6ORGPnkZS/L5w==", + "version": "0.5.10", + "resolved": "https://registry.npmjs.org/@astrojs/check/-/check-0.5.10.tgz", + "integrity": "sha512-vliHXM9cu/viGeKiksUM4mXfO816ohWtawTl2ADPgTsd4nUMjFiyAl7xFZhF34yy4hq4qf7jvK1F2PlR3b5I5w==", "dependencies": { - "@astrojs/language-server": "^2.8.1", + "@astrojs/language-server": "^2.8.4", "chokidar": "^3.5.3", "fast-glob": "^3.3.1", "kleur": "^4.1.5", @@ -56,17 +56,17 @@ "integrity": "sha512-tGmHvrhpzuz0JBHaJX8GywN9g4rldVNHtkoVDC3m/DdzBO70jGoVuc0uuNVglRYnsdwkbG0K02Iw3nOOR3/Y4g==" }, "node_modules/@astrojs/language-server": { - "version": "2.8.3", - "resolved": "https://registry.npmjs.org/@astrojs/language-server/-/language-server-2.8.3.tgz", - "integrity": "sha512-tO47Lcue7OPXfIDbKVDcshwpC13yaWaTVLyiSOnQ2Yng2Z2SgcJf06Cj4xMpJqGp6s7/o/gcQWYUTl2bpkWKig==", + "version": "2.8.4", + "resolved": "https://registry.npmjs.org/@astrojs/language-server/-/language-server-2.8.4.tgz", + "integrity": "sha512-sJH5vGTBkhgA8+hdhzX78UUp4cFz4Mt7xkEkevD188OS5bDMkaue6hK+dtXWM47mnrXFveXA2u38K7S+5+IRjA==", "dependencies": { "@astrojs/compiler": "^2.7.0", "@jridgewell/sourcemap-codec": "^1.4.15", - "@volar/kit": "~2.1.2", - "@volar/language-core": "~2.1.2", - "@volar/language-server": "~2.1.2", - "@volar/language-service": "~2.1.2", - "@volar/typescript": "~2.1.2", + "@volar/kit": "~2.1.5", + "@volar/language-core": "~2.1.5", + "@volar/language-server": "~2.1.5", + "@volar/language-service": "~2.1.5", + "@volar/typescript": "~2.1.5", "fast-glob": "^3.2.12", "volar-service-css": "0.0.34", "volar-service-emmet": "0.0.34", @@ -163,9 +163,9 @@ } }, "node_modules/@astrojs/starlight": { - "version": "0.21.1", - "resolved": "https://registry.npmjs.org/@astrojs/starlight/-/starlight-0.21.1.tgz", - "integrity": "sha512-nQ5EwKnB3eI8jxQrbgzZJJcyxeIiL3GzsAhl//1fE541MlD+PKy53v1PsYPi/RILdjt1Pg39rf1fkJC/rhXRgw==", + "version": "0.21.2", + "resolved": "https://registry.npmjs.org/@astrojs/starlight/-/starlight-0.21.2.tgz", + "integrity": "sha512-ziDfrbhBjw/+HwMITk6yz7SbkQKQJZY9GlaPHntSPq4kYs+b2ru3toIxj2l3T9LUFtUpNWHkj+C1wJTmfLZfaw==", "dependencies": { "@astrojs/mdx": "^2.1.1", "@astrojs/sitemap": "^3.0.5", @@ -224,12 +224,12 @@ } }, "node_modules/@babel/code-frame": { - "version": "7.23.5", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.23.5.tgz", - 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"detect-libc": "^2.0.2", - "semver": "^7.5.4" + "detect-libc": "^2.0.3", + "semver": "^7.6.0" } }, "shebang-command": { @@ -14325,9 +14327,9 @@ "integrity": "sha512-OJabfkAg1WLZSqJAJ0Z6Sdt3utnbzr/jh+NAHoyWHJe8CMSy79Gm085094M9nvTPy22KzTVn5Zq5mbapCI/hPA==" }, "typescript": { - "version": "5.4.2", - "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.4.2.tgz", - "integrity": "sha512-+2/g0Fds1ERlP6JsakQQDXjZdZMM+rqpamFZJEKh4kwTIn3iDkgKtby0CeNd5ATNZ4Ry1ax15TMx0W2V+miizQ==" + "version": "5.4.3", + "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.4.3.tgz", + "integrity": "sha512-KrPd3PKaCLr78MalgiwJnA25Nm8HAmdwN3mYUYZgG/wizIo9EainNVQI9/yDavtVFRN2h3k8uf3GLHuhDMgEHg==" }, "typescript-auto-import-cache": { "version": "0.3.2", @@ -14586,9 +14588,9 @@ "requires": {} }, "vscode-css-languageservice": { - "version": "6.2.12", - "resolved": "https://registry.npmjs.org/vscode-css-languageservice/-/vscode-css-languageservice-6.2.12.tgz", - "integrity": "sha512-PS9r7HgNjqzRl3v91sXpCyZPc8UDotNo6gntFNtGCKPhGA9Frk7g/VjX1Mbv3F00pn56D+rxrFzR9ep4cawOgA==", + "version": "6.2.13", + "resolved": "https://registry.npmjs.org/vscode-css-languageservice/-/vscode-css-languageservice-6.2.13.tgz", + "integrity": "sha512-2rKWXfH++Kxd9Z4QuEgd1IF7WmblWWU7DScuyf1YumoGLkY9DW6wF/OTlhOyO2rN63sWHX2dehIpKBbho4ZwvA==", "requires": { "@vscode/l10n": "^0.0.18", "vscode-languageserver-textdocument": "^1.0.11", @@ -14604,9 +14606,9 @@ } }, "vscode-html-languageservice": { - "version": "5.1.2", - "resolved": "https://registry.npmjs.org/vscode-html-languageservice/-/vscode-html-languageservice-5.1.2.tgz", - "integrity": "sha512-wkWfEx/IIR3s2P5yD4aTGHiOb8IAzFxgkSt1uSC3itJ4oDAm23yG7o0L29JljUdnXDDgLafPAvhv8A2I/8riHw==", + "version": "5.2.0", + "resolved": "https://registry.npmjs.org/vscode-html-languageservice/-/vscode-html-languageservice-5.2.0.tgz", + "integrity": "sha512-cdNMhyw57/SQzgUUGSIMQ66jikqEN6nBNyhx5YuOyj9310+eY9zw8Q0cXpiKzDX8aHYFewQEXRnigl06j/TVwQ==", "requires": { "@vscode/l10n": "^0.0.18", "vscode-languageserver-textdocument": "^1.0.11", diff --git a/docs/package.json b/docs/package.json index 216c54983f..a3892baa6d 100644 --- a/docs/package.json +++ b/docs/package.json @@ -11,10 +11,10 @@ "format": "prettier --write ." }, "dependencies": { - "@astrojs/check": "^0.5.9", - "@astrojs/starlight": "^0.21.1", - "astro": "^4.5.6", - "sharp": "^0.33.2", - "typescript": "^5.4.2" + "@astrojs/check": "^0.5.10", + "@astrojs/starlight": "^0.21.2", + "astro": "^4.5.9", + "sharp": "^0.33.3", + "typescript": "^5.4.3" } } From b0523ad9c034806a44b01b377d58c2f62612a311 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 27 Mar 2024 00:02:03 +0100 Subject: [PATCH 04/10] feat(silo-prepro): use hash instead of line count to test for equality (#1488) See discussion: https://loculus.slack.com/archives/C05G172HL6L/p1711384380415999 --- kubernetes/loculus/silo_import_job.sh | 81 +++++++++++++++------------ 1 file changed, 44 insertions(+), 37 deletions(-) diff --git a/kubernetes/loculus/silo_import_job.sh b/kubernetes/loculus/silo_import_job.sh index 1601e3b4d2..b236aa8221 100755 --- a/kubernetes/loculus/silo_import_job.sh +++ b/kubernetes/loculus/silo_import_job.sh @@ -2,6 +2,12 @@ set -e +base_data_dir="/preprocessing/input" +output_data_dir="/preprocessing/output" +current_timestamp=$(date +%s) +current_input_data_dir="$base_data_dir/$current_timestamp" +old_input_data_dir="$base_data_dir"/$(ls -1 "$base_data_dir" | sort -n | grep -E '^[0-9]+$' | tail -n 1) + get_token() { if [ -z "$KEYCLOAK_TOKEN_URL" ]; then echo "KEYCLOAK_TOKEN_URL is not set" @@ -35,90 +41,91 @@ get_token() { echo } -download_data() { - base_data_dir="/preprocessing/input" - last_timestamp_dir=$(ls -1 "$base_data_dir" | sort -n | grep -E '^[0-9]+$' | tail -n 1) +delete_all_input() { + echo "Deleting all input data" + rm -f "$base_data_dir/data.ndjson" + rm -rf "$current_input_data_dir" + echo +} - current_timestamp=$(date +%s) - echo "checking for current timestamp $current_timestamp" +download_data() { - data_dir="$base_data_dir/$current_timestamp" - mkdir -p "$data_dir" - echo "created $data_dir" + mkdir -p "$current_input_data_dir" + echo "created $current_input_data_dir" released_data_endpoint="$BACKEND_BASE_URL/get-released-data" echo "calling $released_data_endpoint" set +e - curl -o "$data_dir/data.ndjson" --fail-with-body "$released_data_endpoint" -H "Authorization: Bearer $jwt" + curl -o "$current_input_data_dir/data.ndjson" --fail-with-body "$released_data_endpoint" -H "Authorization: Bearer $jwt" exit_code=$? set -e if [ $exit_code -ne 0 ]; then echo "Curl command failed with exit code $exit_code, cleaning up and exiting." - rm -rf "$data_dir" + rm -rf "$current_input_data_dir" exit $exit_code fi - echo "downloaded $(wc -l < "$data_dir/data.ndjson") sequences" + echo "downloaded $(wc -l < "$current_input_data_dir/data.ndjson") sequences" echo - echo "checking for last timestamp dir $last_timestamp_dir" - if [[ "$last_timestamp_dir" =~ ^[0-9]+$ ]]; then - last_number_of_sequences=$(wc -l < "$base_data_dir/$last_timestamp_dir/data.ndjson") - - echo "old data file $last_timestamp_dir has $last_number_of_sequences lines" - new_number_of_sequences=$(wc -l < "$data_dir/data.ndjson") - echo "new data file '$data_dir/data.ndjson' has $new_number_of_sequences lines" - echo - if [ "$last_number_of_sequences" -eq "$new_number_of_sequences" ]; then - echo "last data.ndjson has same line count, deleting current data dir" - rm -rf "$data_dir" + echo "Sorting downloaded data.ndjson" + + echo "checking for old input data dir $old_input_data_dir" + if [[ "$old_input_data_dir" =~ ^[0-9]+$ ]]; then + old_hash=$(md5sum < "$current_input_data_dir/data.ndjson" | awk '{print $1}') + new_hash=$(md5sum < "$current_input_data_dir/data.ndjson" | awk '{print $1}') + echo "old hash: $old_hash" + echo "new hash: $new_hash" + if [ "$new_hash" = "$old_hash" ]; then + echo "Hashes are equal, skipping preprocessing" + echo "Deleting input data dir $current_input_data_dir" + rm -rf "$current_input_data_dir" exit 0 else - echo "last data.ndjson has less line count, deleting older data dir" - rm -rf "${base_data_dir}/${last_timestamp_dir:?}" + echo "Hashes are unequal, deleting old input data dir" + rm -rf "$old_input_data_dir:?}" fi fi echo } preprocessing() { - if [ -s "$data_dir/data.ndjson" ]; then + # TODO: #1489 Remove emptiness test once https://github.com/GenSpectrum/LAPIS-SILO/issues/244 fixed + if [ -s "$current_input_data_dir" ]; then echo "data.ndjson is not empty, starting preprocessing" rm -f "$base_data_dir/data.ndjson" - cp "$data_dir/data.ndjson" "$base_data_dir/data.ndjson" + cp "$current_input_data_dir/data.ndjson" "$base_data_dir/data.ndjson" set +e - /app/siloApi --preprocessing + time /app/siloApi --preprocessing exit_code=$? set -e if [ $exit_code -ne 0 ]; then - echo "SiloApi command failed with exit code $exit_code, cleaning up and exiting." - - rm -rf "$data_dir" - rm -f "$base_data_dir/data.ndjson" - + echo "SiloApi command failed with exit code $exit_code, cleaning up and exiting." + delete_all_input exit $exit_code fi echo "preprocessing for $current_timestamp done" else - echo "skipping empty data.ndjson, deleting directory" - rm -rf "$data_dir" + echo "empty data.ndjson, deleting all input" + delete_all_input + fi echo } cleanup_output_data() { output_data_dir="/preprocessing/output" - echo "cleaning up output data dir $output_data_dir" + echo "Removing all but the most recent output directory in $output_data_dir" cd $output_data_dir || exit - if [ -n "$(ls -d */ 2>/dev/null)" ]; then - directories=$(ls -dt */) + if [ -n "$(ls -d -- */ 2>/dev/null)" ]; then + directories=$(ls -dt -- */) if [ "$(echo "$directories" | wc -l)" -gt 1 ]; then newest_dir=$(echo "$directories" | head -n 1) echo "$directories" | tail -n +2 | xargs rm -r From c47f0d78444f55febadf70a9cd7844b21fef5ddc Mon Sep 17 00:00:00 2001 From: lukepereira Date: Tue, 26 Mar 2024 19:19:17 -0400 Subject: [PATCH 05/10] feat(website): Misc SeqSet UI updates (#1493) --- .../SeqSetCitations/ExportSeqSet.tsx | 3 +- .../components/SeqSetCitations/SeqSetForm.tsx | 12 +++-- .../components/SeqSetCitations/SeqSetItem.tsx | 44 +++++++++++++++---- .../components/SeqSetCitations/SeqSetList.tsx | 2 +- website/src/pages/seqsets/[seqSetId].astro | 41 +++++++++-------- .../tests/pages/seqsets/[seqSetId].spec.ts | 2 +- website/tests/pages/seqsets/index.spec.ts | 2 +- 7 files changed, 68 insertions(+), 38 deletions(-) diff --git a/website/src/components/SeqSetCitations/ExportSeqSet.tsx b/website/src/components/SeqSetCitations/ExportSeqSet.tsx index f17783aabe..77d94544ff 100644 --- a/website/src/components/SeqSetCitations/ExportSeqSet.tsx +++ b/website/src/components/SeqSetCitations/ExportSeqSet.tsx @@ -103,7 +103,7 @@ export const ExportSeqSet: FC = ({ seqSet, seqSetRecords }) = autoHideDuration={2000} message='Copied to clipboard' /> -
+
@@ -204,6 +204,7 @@ export const ExportSeqSet: FC = ({ seqSet, seqSetRecords }) = rows={5} cols={40} value={getSelectedCitationText()} + readOnly />
diff --git a/website/src/components/SeqSetCitations/SeqSetForm.tsx b/website/src/components/SeqSetCitations/SeqSetForm.tsx index df79d285de..10aaec673c 100644 --- a/website/src/components/SeqSetCitations/SeqSetForm.tsx +++ b/website/src/components/SeqSetCitations/SeqSetForm.tsx @@ -126,15 +126,15 @@ export const SeqSetForm: FC = ({ clientConfig, accessToken, edi
-

{`${editSeqSet ? 'Edit' : 'Create'} SeqSet`}

+

{`${editSeqSet ? 'Edit' : 'Create a'} SeqSet`}

-
-
+
+
= ({ clientConfig, accessToken, edi maxLength={255} />
-

Accessions

- {Object.keys(accessionsInput).map((type) => (