diff --git a/.github/workflows/website-tests.yml b/.github/workflows/website-tests.yml index 904982384..b0d31fa45 100644 --- a/.github/workflows/website-tests.yml +++ b/.github/workflows/website-tests.yml @@ -35,7 +35,7 @@ jobs: - run: npm ci - run: npm run check-format - run: npm run check-types - + if: always() unitTests: name: Unit Tests runs-on: codebuild-loculus-ci-${{ github.run_id }}-${{ github.run_attempt }} diff --git a/backend/build.gradle b/backend/build.gradle index bb24dcb3c..cdc603bd9 100644 --- a/backend/build.gradle +++ b/backend/build.gradle @@ -40,7 +40,7 @@ dependencies { implementation "org.jetbrains.exposed:exposed-jdbc:0.50.1" implementation "org.jetbrains.exposed:exposed-json:0.50.1" implementation "org.jetbrains.exposed:exposed-kotlin-datetime:0.50.1" - implementation "org.jetbrains.kotlinx:kotlinx-datetime:0.5.0" + implementation "org.jetbrains.kotlinx:kotlinx-datetime:0.6.0" implementation "org.hibernate.validator:hibernate-validator:8.0.1.Final" implementation "org.keycloak:keycloak-admin-client:23.0.7" diff --git a/deploy.py b/deploy.py index 6cd6a52b4..ae132cc5a 100755 --- a/deploy.py +++ b/deploy.py @@ -188,6 +188,10 @@ def get_codespace_name(): def generate_configs(from_live=False): TEMP_DIR.mkdir(parents=True, exist_ok=True) + # Delete all files in the temp directory + for file in TEMP_DIR.iterdir(): + file.unlink() + helm_chart = str(HELM_CHART_DIR) codespace_name = get_codespace_name() @@ -202,11 +206,24 @@ def generate_configs(from_live=False): runtime_config_path = TEMP_DIR / 'runtime_config.json' generate_config(helm_chart, 'templates/loculus-website-config.yaml', runtime_config_path, codespace_name, from_live) + ingest_configmap_path = TEMP_DIR / 'config.yaml' + ingest_template_path = 'templates/loculus-ingest-config.yaml' + ingest_configout_path = TEMP_DIR / 'ingest-config.yaml' + generate_config(helm_chart, ingest_template_path, ingest_configmap_path, codespace_name, from_live, ingest_configout_path) + + prepro_configmap_path = TEMP_DIR / 'preprocessing-config.yaml' + prepro_template_path = 'templates/loculus-preprocessing-config.yaml' + prepro_configout_path = TEMP_DIR / 'preprocessing-config.yaml' + generate_config(helm_chart, prepro_template_path, prepro_configmap_path, codespace_name, from_live, prepro_configout_path) + run_command(['python3', 'kubernetes/config-processor/config-processor.py', TEMP_DIR, output_dir]) -def generate_config(helm_chart, template, output_path, codespace_name=None, from_live=False): +def generate_config(helm_chart, template, configmap_path, codespace_name=None, from_live=False, output_path=None): helm_template_cmd = ['helm', 'template', 'name-does-not-matter', helm_chart, '--show-only', template] + if not output_path: + output_path = configmap_path + if codespace_name: helm_template_cmd.extend(['--set', 'codespaceName='+codespace_name]) @@ -219,17 +236,25 @@ def generate_config(helm_chart, template, output_path, codespace_name=None, from helm_template_cmd.extend(['--set', 'usePublicRuntimeConfigAsServerSide=true']) else: helm_template_cmd.extend(['--set', 'environment=local']) + helm_template_cmd.extend(['--set', 'testconfig=true']) helm_output = run_command(helm_template_cmd, capture_output=True, text=True).stdout if args.dry_run: return - parsed_yaml = yaml.safe_load(helm_output) - config_data = parsed_yaml['data'][output_path.name] + parsed_yaml = list(yaml.full_load_all(helm_output)) + if len(parsed_yaml) == 1: + config_data = parsed_yaml[0]['data'][configmap_path.name] - with open(output_path, 'w') as f: - f.write(config_data) + with open(output_path, 'w') as f: + f.write(config_data) - print(f"Wrote config to {output_path}") + print(f"Wrote config to {output_path}") + elif any(substring in template for substring in ["ingest", "preprocessing"]): + for doc in parsed_yaml: + config_data = yaml.safe_load(doc['data'][configmap_path.name]) + with open(output_path.with_suffix(f'.{config_data["organism"]}.yaml'), 'w') as f: + yaml.dump(config_data, f) + print(f"Wrote config to {f.name}") def install_secret_generator(): add_helm_repo_command = [ diff --git a/docs/package-lock.json b/docs/package-lock.json index da01c96bc..94483d082 100644 --- a/docs/package-lock.json +++ b/docs/package-lock.json @@ -8,10 +8,10 @@ "name": "docs2", "version": "0.0.1", "dependencies": { - "@astrojs/check": "^0.6.0", - "@astrojs/starlight": "^0.22.2", + "@astrojs/check": "^0.7.0", + "@astrojs/starlight": "^0.23.1", "astro": "^4.8.3", - "sharp": "^0.33.3", + "sharp": "^0.33.4", "typescript": "^5.4.5" } }, @@ -28,11 +28,11 @@ } }, "node_modules/@astrojs/check": { - "version": "0.6.0", - "resolved": "https://registry.npmjs.org/@astrojs/check/-/check-0.6.0.tgz", - "integrity": "sha512-Q6fct7FvByTf0L5lvH2QwFelXtLViWhPNgMfOvrGq7spV5SPX9jQPoFxH+nRFh1oDhBBIWImRjkSpSyhX9fQHA==", + "version": "0.7.0", + "resolved": "https://registry.npmjs.org/@astrojs/check/-/check-0.7.0.tgz", + "integrity": 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"https://registry.npmjs.org/shikiji/-/shikiji-0.9.19.tgz", - "integrity": "sha512-Kw2NHWktdcdypCj1GkKpXH4o6Vxz8B8TykPlPuLHOGSV8VkhoCLcFOH4k19K4LXAQYRQmxg+0X/eM+m2sLhAkg==", - "requires": { - "shikiji-core": "0.9.19" - } - }, - "shikiji-core": { - "version": "0.9.19", - "resolved": "https://registry.npmjs.org/shikiji-core/-/shikiji-core-0.9.19.tgz", - "integrity": "sha512-AFJu/vcNT21t0e6YrfadZ+9q86gvPum6iywRyt1OtIPjPFe25RQnYJyxHQPMLKCCWA992TPxmEmbNcOZCAJclw==" - }, "signal-exit": { "version": "4.1.0", "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-4.1.0.tgz", @@ -12759,9 +13110,9 @@ "requires": {} }, "volar-service-css": { - "version": "0.0.43", - "resolved": "https://registry.npmjs.org/volar-service-css/-/volar-service-css-0.0.43.tgz", - "integrity": "sha512-rg2gTXhswq6Wz8euZgCRS68+7EPH+3R7SeTqYfAAtHKoU0rS1bwdxP1CWHezyxnHrLMiXEypCgJJWcMTay3W7g==", + "version": "0.0.45", + "resolved": "https://registry.npmjs.org/volar-service-css/-/volar-service-css-0.0.45.tgz", + "integrity": "sha512-f+AlUI1+kESbcZSVaNJVAnK0c/9Da5StoxzPqA5/8VqUHJWNdubWNnwG5xpFVTfgh6pgTcey3UBhBfHytFaIOg==", "requires": { "vscode-css-languageservice": "^6.2.10", "vscode-languageserver-textdocument": "^1.0.11", @@ -12769,36 +13120,19 @@ } }, "volar-service-emmet": { - "version": "0.0.43", - "resolved": "https://registry.npmjs.org/volar-service-emmet/-/volar-service-emmet-0.0.43.tgz", - "integrity": "sha512-ODsSOsSScVTNSD1Z+e4EV21RuN3q38ahGnuyxKYHW9Fg0RwfLatHl6wIRfj21XlVVa8twBMsA/Fp43ObuDEBxQ==", + "version": "0.0.45", + "resolved": "https://registry.npmjs.org/volar-service-emmet/-/volar-service-emmet-0.0.45.tgz", + "integrity": "sha512-9nLXSDkR1vA/3fQkFEsSXAu3XovQxOpTkVG2jilQgfek/K1ZLkaA/WMhN/TtmPmQg4NxE9Ni6mA5udBQ5gVXIA==", "requires": { - "@vscode/emmet-helper": "^2.9.2", - "vscode-html-languageservice": "npm:@johnsoncodehk/vscode-html-languageservice@5.2.0-34a5462" - }, - "dependencies": { - "@vscode/l10n": { - "version": "0.0.18", - "resolved": 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"sha512-+mBS2EsDgp/kunKEBnHvhBwIQm5v2ahw4NKpKdg4sTpXy3UxqHt+Fq/wRYQ7Z8LlNVNRVfp75ThjM+w2zaZBAw==", "requires": { "vscode-uri": "^3.0.8" } }, "volar-service-typescript": { - "version": "0.0.43", - "resolved": "https://registry.npmjs.org/volar-service-typescript/-/volar-service-typescript-0.0.43.tgz", - "integrity": "sha512-oXYZHuM7QYBmgSiheFkoQPyUzzvm9ddaUzfDqc9cOM+fDuMAkUer2bEqnqZXerGjhsjuXNCu4PGlSOJJMxWe3A==", + "version": "0.0.45", + "resolved": "https://registry.npmjs.org/volar-service-typescript/-/volar-service-typescript-0.0.45.tgz", + "integrity": "sha512-i/mMIIAMastJ2kgPo3qvX0Rrl7NyxhIYZ0ug/B4ambZcLPI1vzBgS2fmvyWX3jhBYHh8NmbAotFj+0Y9JtN47A==", "requires": { "path-browserify": "^1.0.1", "semver": "^7.5.4", @@ -12844,9 +13178,9 @@ } }, "volar-service-typescript-twoslash-queries": { - "version": "0.0.43", - "resolved": "https://registry.npmjs.org/volar-service-typescript-twoslash-queries/-/volar-service-typescript-twoslash-queries-0.0.43.tgz", - "integrity": "sha512-FUqgvK2a6YxNO0P+zmY5syVatD8I7+qEA+mj1lotqQxwtY0Gh3UDCCqTVapX1E4VxF/pvNac7eVOBkCUVVZC5w==", + "version": "0.0.45", + "resolved": "https://registry.npmjs.org/volar-service-typescript-twoslash-queries/-/volar-service-typescript-twoslash-queries-0.0.45.tgz", + "integrity": "sha512-KrPUUvKggZgV9mrDpstCzmf20irgv0ooMv+FGDzIIQUkya+d2+nSS8Mx2h9FvsYgLccUVw5jU3Rhwhd3pv/7qg==", "requires": {} }, "vscode-css-languageservice": { diff --git a/docs/package.json b/docs/package.json index 6e298130d..efb4b611a 100644 --- a/docs/package.json +++ b/docs/package.json @@ -11,10 +11,10 @@ "format": "prettier --write ." }, "dependencies": { - "@astrojs/check": "^0.6.0", - "@astrojs/starlight": "^0.22.2", + "@astrojs/check": "^0.7.0", + "@astrojs/starlight": "^0.23.1", "astro": "^4.8.3", - "sharp": "^0.33.3", + "sharp": "^0.33.4", "typescript": "^5.4.5" } } diff --git a/ingest/environment.yml b/ingest/environment.yml index c91a13001..bb25aefc9 100644 --- a/ingest/environment.yml +++ b/ingest/environment.yml @@ -10,7 +10,7 @@ dependencies: - biopython - click - jsonlines - - ncbi-datasets-cli >=16.15.0 + - ncbi-datasets-cli >=16.17.1 - pandas - PyYAML - requests diff --git a/kubernetes/config-processor/config-processor.py b/kubernetes/config-processor/config-processor.py index 2ca4887f0..1261ae190 100644 --- a/kubernetes/config-processor/config-processor.py +++ b/kubernetes/config-processor/config-processor.py @@ -1,7 +1,8 @@ import os +import re import shutil + import requests -import re def copy_structure(input_dir, output_dir): @@ -11,6 +12,8 @@ def copy_structure(input_dir, output_dir): os.makedirs(dir_path, exist_ok=True) for file in files: file_path = os.path.join(output_dir, os.path.relpath(os.path.join(root, file), input_dir)) + # Make sure the directory exists + os.makedirs(os.path.dirname(file_path), exist_ok=True) shutil.copy(os.path.join(root, file), file_path) def replace_url_with_content(file_content): diff --git a/kubernetes/loculus/templates/loculus-preprocessing-config.yaml b/kubernetes/loculus/templates/loculus-preprocessing-config.yaml index cd3101d64..348a27848 100644 --- a/kubernetes/loculus/templates/loculus-preprocessing-config.yaml +++ b/kubernetes/loculus/templates/loculus-preprocessing-config.yaml @@ -8,7 +8,8 @@ metadata: name: loculus-preprocessing-config-{{ $organism }}-v{{ $processingConfig.version }}-{{ $processingIndex }} data: preprocessing-config.yaml: | - {{- $processingConfig.configFile | toYaml | nindent 4 -}} + {{- $processingConfig.configFile | toYaml | nindent 4 }} + organism: {{ $organism }} {{- end }} {{- end }} {{- end }} \ No newline at end of file diff --git a/preprocessing/dummy/requirements.txt b/preprocessing/dummy/requirements.txt index cac42430e..fa619d8e4 100644 --- a/preprocessing/dummy/requirements.txt +++ b/preprocessing/dummy/requirements.txt @@ -1,5 +1,5 @@ certifi==2023.7.22 charset-normalizer==3.2.0 idna==3.7 -requests==2.31.0 +requests==2.32.0 urllib3==2.0.7 diff --git a/preprocessing/nextclade/src/loculus_preprocessing/config.py b/preprocessing/nextclade/src/loculus_preprocessing/config.py index 33a319dd7..7ee23cd71 100644 --- a/preprocessing/nextclade/src/loculus_preprocessing/config.py +++ b/preprocessing/nextclade/src/loculus_preprocessing/config.py @@ -17,10 +17,10 @@ @dataclass class Config: - backend_host: str = "http://127.0.0.1:8079" - keycloak_host: str = "http://172.0.0.1:8083" + backend_host: str = "http://127.0.0.1:8079/ebola-zaire" + keycloak_host: str = "http://127.0.0.1:8083" keycloak_user: str = "preprocessing_pipeline" - keycloak_password: str = "" + keycloak_password: str = "preprocessing_pipeline" keycloak_token_path: str = "realms/loculus/protocol/openid-connect/token" nextclade_dataset_name: str = "nextstrain/mpox/all-clades" nextclade_dataset_tag: str | None = None diff --git a/website/package-lock.json b/website/package-lock.json index 58497de34..2a74e5fc6 100644 --- a/website/package-lock.json +++ b/website/package-lock.json @@ -19,10 +19,10 @@ "@tanstack/react-query": "^4.36.1", "@zodios/core": "^10.9.6", "@zodios/react": "^10.4.5", - "astro": "^4.8.3", - "axios": "^1.6.8", + "astro": "^4.8.6", + "axios": "^1.7.1", "change-case": "~5.3.0", - "chart.js": "^4.4.2", + "chart.js": "^4.4.3", "cookie": "^0.6.0", "flowbite-react": "^0.9.0", "jsonwebtoken": "^9.0.2", @@ -37,17 +37,17 @@ "react-dom": "^18.3.1", "react-toastify": "^10.0.5", "react-tooltip": "^5.26.4", - "rsuite": "^5.60.2", + "rsuite": "^5.61.0", "unplugin-icons": "^0.19.0", "winston": "^3.13.0", "zod": "^3.23.6" }, "devDependencies": { - "@astrojs/check": "^0.6.0", + "@astrojs/check": "^0.7.0", "@astrojs/react": "^3.3.4", "@astrojs/tailwind": "^5.1.0", "@emotion/styled": "^11.11.5", - "@iconify/json": "^2.2.209", + "@iconify/json": "^2.2.212", "@playwright/test": "^1.44.0", "@tailwindcss/forms": "^0.5.7", "@tanstack/eslint-plugin-query": "^5.35.6", @@ -56,14 +56,14 @@ "@testing-library/react": "^15.0.7", 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"@volar/language-service": { @@ -16444,29 +16476,10 @@ } } }, - "node_modules/volar-service-emmet/node_modules/@vscode/l10n": { - "version": "0.0.18", - "resolved": "https://registry.npmjs.org/@vscode/l10n/-/l10n-0.0.18.tgz", - "integrity": "sha512-KYSIHVmslkaCDyw013pphY+d7x1qV8IZupYfeIfzNA+nsaWHbn5uPuQRvdRFsa9zFzGeudPuoGoZ1Op4jrJXIQ==", - "dev": true - }, - "node_modules/volar-service-emmet/node_modules/vscode-html-languageservice": { - "name": "@johnsoncodehk/vscode-html-languageservice", - "version": "5.2.0-34a5462", - "resolved": "https://registry.npmjs.org/@johnsoncodehk/vscode-html-languageservice/-/vscode-html-languageservice-5.2.0-34a5462.tgz", - "integrity": "sha512-etqLfpSJ5zaw76KUNF603be6d6QsiQPmaHr9FKEp4zhLZJzWCCMH6Icak7MtLUFLZLMpL761mZNImi/joBo1ZA==", - "dev": true, - "dependencies": { - "@vscode/l10n": "^0.0.18", - "vscode-languageserver-textdocument": "^1.0.11", - "vscode-languageserver-types": "^3.17.5", - "vscode-uri": "^3.0.8" - } - }, "node_modules/volar-service-html": { - "version": "0.0.43", - "resolved": "https://registry.npmjs.org/volar-service-html/-/volar-service-html-0.0.43.tgz", - "integrity": "sha512-Z/S7SCkHmpoR708WTQLCE3k+hfT16xjMfq9Htv7Y3yJeykah1jZO8oZX3433OPFfbS/ZFbGa2VlAIgDTVRU5Pg==", + "version": "0.0.45", + "resolved": "https://registry.npmjs.org/volar-service-html/-/volar-service-html-0.0.45.tgz", + "integrity": "sha512-tLTJqfy1v5C4nmeAsfekFIKPl4r4qDMyL0L9MWywr/EApZzPCsbeUGxCqdzxSMC2q7PMCfX2i167txDo+J0LVA==", "dev": true, "dependencies": { "vscode-html-languageservice": "npm:@johnsoncodehk/vscode-html-languageservice@5.2.0-34a5462", @@ -16474,7 +16487,7 @@ "vscode-uri": "^3.0.8" }, "peerDependencies": { - "@volar/language-service": "~2.2.0" + "@volar/language-service": "~2.2.3" }, "peerDependenciesMeta": { "@volar/language-service": { @@ -16502,15 +16515,15 @@ } }, "node_modules/volar-service-prettier": { - "version": "0.0.43", - "resolved": "https://registry.npmjs.org/volar-service-prettier/-/volar-service-prettier-0.0.43.tgz", - "integrity": "sha512-Beq+iNyG05PlSPTISOFK5Yoj29rXdGb6htvyFk2u0jVFRGX1QD0Pb5ze9OiqfUVwT+3cFZhPrSPndbTR1ft/aA==", + "version": "0.0.45", + "resolved": "https://registry.npmjs.org/volar-service-prettier/-/volar-service-prettier-0.0.45.tgz", + "integrity": "sha512-+mBS2EsDgp/kunKEBnHvhBwIQm5v2ahw4NKpKdg4sTpXy3UxqHt+Fq/wRYQ7Z8LlNVNRVfp75ThjM+w2zaZBAw==", "dev": true, "dependencies": { "vscode-uri": "^3.0.8" }, "peerDependencies": { - "@volar/language-service": "~2.2.0", + "@volar/language-service": "~2.2.3", "prettier": "^2.2 || ^3.0" }, "peerDependenciesMeta": { @@ -16523,9 +16536,9 @@ } }, "node_modules/volar-service-typescript": { - "version": "0.0.43", - "resolved": "https://registry.npmjs.org/volar-service-typescript/-/volar-service-typescript-0.0.43.tgz", - "integrity": "sha512-oXYZHuM7QYBmgSiheFkoQPyUzzvm9ddaUzfDqc9cOM+fDuMAkUer2bEqnqZXerGjhsjuXNCu4PGlSOJJMxWe3A==", + "version": "0.0.45", + "resolved": "https://registry.npmjs.org/volar-service-typescript/-/volar-service-typescript-0.0.45.tgz", + "integrity": "sha512-i/mMIIAMastJ2kgPo3qvX0Rrl7NyxhIYZ0ug/B4ambZcLPI1vzBgS2fmvyWX3jhBYHh8NmbAotFj+0Y9JtN47A==", "dev": true, "dependencies": { "path-browserify": "^1.0.1", @@ -16535,7 +16548,7 @@ "vscode-nls": "^5.2.0" }, "peerDependencies": { - "@volar/language-service": "~2.2.0" + "@volar/language-service": "~2.2.3" }, "peerDependenciesMeta": { "@volar/language-service": { @@ -16544,12 +16557,12 @@ } }, "node_modules/volar-service-typescript-twoslash-queries": { - "version": "0.0.43", - "resolved": "https://registry.npmjs.org/volar-service-typescript-twoslash-queries/-/volar-service-typescript-twoslash-queries-0.0.43.tgz", - "integrity": "sha512-FUqgvK2a6YxNO0P+zmY5syVatD8I7+qEA+mj1lotqQxwtY0Gh3UDCCqTVapX1E4VxF/pvNac7eVOBkCUVVZC5w==", + "version": "0.0.45", + "resolved": "https://registry.npmjs.org/volar-service-typescript-twoslash-queries/-/volar-service-typescript-twoslash-queries-0.0.45.tgz", + "integrity": "sha512-KrPUUvKggZgV9mrDpstCzmf20irgv0ooMv+FGDzIIQUkya+d2+nSS8Mx2h9FvsYgLccUVw5jU3Rhwhd3pv/7qg==", "dev": true, "peerDependencies": { - "@volar/language-service": "~2.2.0" + "@volar/language-service": "~2.2.3" }, "peerDependenciesMeta": { "@volar/language-service": { diff --git a/website/package.json b/website/package.json index b8a60762c..d716bd84a 100644 --- a/website/package.json +++ b/website/package.json @@ -31,10 +31,10 @@ "@tanstack/react-query": "^4.36.1", "@zodios/core": "^10.9.6", "@zodios/react": "^10.4.5", - "astro": "^4.8.3", - "axios": "^1.6.8", + "astro": "^4.8.6", + "axios": "^1.7.1", "change-case": "~5.3.0", - "chart.js": "^4.4.2", + "chart.js": "^4.4.3", "cookie": "^0.6.0", "flowbite-react": "^0.9.0", "jsonwebtoken": "^9.0.2", @@ -49,17 +49,17 @@ "react-dom": "^18.3.1", "react-toastify": "^10.0.5", "react-tooltip": "^5.26.4", - "rsuite": "^5.60.2", + "rsuite": "^5.61.0", "unplugin-icons": "^0.19.0", "winston": "^3.13.0", "zod": "^3.23.6" }, "devDependencies": { - "@astrojs/check": "^0.6.0", + "@astrojs/check": "^0.7.0", "@astrojs/react": "^3.3.4", "@astrojs/tailwind": "^5.1.0", "@emotion/styled": "^11.11.5", - "@iconify/json": "^2.2.209", + "@iconify/json": "^2.2.212", "@playwright/test": "^1.44.0", "@tailwindcss/forms": "^0.5.7", "@tanstack/eslint-plugin-query": "^5.35.6", @@ -68,14 +68,14 @@ "@testing-library/react": "^15.0.7", "@testing-library/user-event": "^14.5.2", "@types/jsonwebtoken": "^9.0.6", - "@types/lodash": "^4.17.1", + "@types/lodash": "^4.17.4", "@types/luxon": "^3.4.2", - "@types/node": "^20.12.11", + "@types/node": "^20.12.12", "@types/react": "^18.3.2", "@types/react-dom": "^18.3.0", "@types/uuid": "^9.0.8", - "@typescript-eslint/eslint-plugin": "^7.9.0", - "@typescript-eslint/parser": "^7.9.0", + "@typescript-eslint/eslint-plugin": "^7.10.0", + "@typescript-eslint/parser": "^7.10.0", "@vitejs/plugin-react": "^4.2.1", "cross-env": "^7.0.3", "daisyui": "^4.11.1", @@ -90,7 +90,7 @@ "msw": "^2.3.0", "prettier": "3.2.5", "prettier-plugin-astro": "^0.13.0", - "sass": "^1.77.1", + "sass": "^1.77.2", "tailwindcss": "^3.4.3", "typescript": "^5.4.5", "uuid": "^9.0.1", diff --git a/website/src/components/IndexPage/OrganismCard.astro b/website/src/components/IndexPage/OrganismCard.astro new file mode 100644 index 000000000..850555d10 --- /dev/null +++ b/website/src/components/IndexPage/OrganismCard.astro @@ -0,0 +1,27 @@ +--- +import type { OrganismStatistics } from './getOrganismStatistics'; +import { routes } from '../../routes/routes'; + +interface Props { + key: string; + image: string | undefined; + displayName: string; + organismStatistics: OrganismStatistics; + numberDaysAgoStatistics: number; +} + +const { key, image, displayName, organismStatistics, numberDaysAgoStatistics } = Astro.props; +--- + + + {image !== undefined && {displayName}} +

{displayName}

+

+ {organismStatistics.totalSequences} sequences
+ (+{organismStatistics.recentSequences} in last {numberDaysAgoStatistics} days)
+ {organismStatistics.lastUpdatedAt && <>Last updated {organismStatistics.lastUpdatedAt.toRelative()}} +

+ diff --git a/website/src/components/IndexPage/getOrganismStatistics.ts b/website/src/components/IndexPage/getOrganismStatistics.ts new file mode 100644 index 000000000..2743dc501 --- /dev/null +++ b/website/src/components/IndexPage/getOrganismStatistics.ts @@ -0,0 +1,71 @@ +import { DateTime, FixedOffsetZone } from 'luxon'; + +import { LapisClient } from '../../services/lapisClient.ts'; +import { RELEASED_AT_FIELD } from '../../settings.ts'; + +export type OrganismStatistics = { + totalSequences: number; + recentSequences: number; + lastUpdatedAt: DateTime | undefined; +}; +type OrganismStatisticsMap = Map; + +export const getOrganismStatisticsMap = async ( + organismNames: string[], + numberDaysAgo: number, +): Promise => { + const statistics = await Promise.all( + organismNames.map((organism) => getOrganismStatistics(organism, numberDaysAgo)), + ); + const result = new Map(); + for (let i = 0; i < organismNames.length; i++) { + result.set(organismNames[i], statistics[i]); + } + return result; +}; + +const getOrganismStatistics = async (organism: string, numberDaysAgo: number): Promise => { + const [{ total, lastUpdatedAt }, recent] = await Promise.all([ + getTotalAndLastUpdatedAt(organism), + getRecent(organism, numberDaysAgo), + ]); + return { + totalSequences: total, + recentSequences: recent, + lastUpdatedAt, + }; +}; + +const getTotalAndLastUpdatedAt = async ( + organism: string, +): Promise<{ total: number; lastUpdatedAt: DateTime | undefined }> => { + const client = LapisClient.createForOrganism(organism); + return ( + await client.call('aggregated', { + version: 1, + }) + ) + .map((x) => ({ + total: x.data[0].count, + lastUpdatedAt: DateTime.fromSeconds(Number.parseInt(x.info.dataVersion, 10), { + zone: FixedOffsetZone.utcInstance, + }), + })) + .unwrapOr({ + total: 0, + lastUpdatedAt: undefined, + }); +}; + +const getRecent = async (organism: string, numberDaysAgo: number): Promise => { + const recentTimestamp = Math.floor(Date.now() / 1000 - numberDaysAgo * 24 * 60 * 60); + const client = LapisClient.createForOrganism(organism); + return ( + await client.call('aggregated', { + [`${RELEASED_AT_FIELD}From`]: recentTimestamp, + version: 1, + }) + ) + .map((x) => x.data[0].count) + .unwrapOr(0); +}; diff --git a/website/src/components/SearchPage/SearchFullUI.tsx b/website/src/components/SearchPage/SearchFullUI.tsx index 0aff747e2..b4eede934 100644 --- a/website/src/components/SearchPage/SearchFullUI.tsx +++ b/website/src/components/SearchPage/SearchFullUI.tsx @@ -230,6 +230,7 @@ export const InnerSearchFullUI = ({ myGroups={myGroups} isHalfScreen={previewHalfScreen} setIsHalfScreen={setPreviewHalfScreen} + setPreviewedSeqId={setPreviewedSeqId} />
void; + setPreviewedSeqId?: (seqId: string | null) => void; } export const SeqPreviewModal: React.FC = ({ @@ -34,6 +36,7 @@ export const SeqPreviewModal: React.FC = ({ myGroups, isHalfScreen = false, setIsHalfScreen, + setPreviewedSeqId, }) => { const [isLoading, setIsLoading] = useState(true); const [data, setData] = useState(null); @@ -73,6 +76,13 @@ export const SeqPreviewModal: React.FC = ({
{seqId}
+ {data !== null && data?.sequenceEntryHistory !== undefined && data?.sequenceEntryHistory.length > 1 && ( + + )}