chore: update prod from main by github-actions[bot] · Pull Request #1133 · GenSpectrum/dashboards

github-actions · 2026-04-08T11:43:11Z

This pull request updates the prod branch with the latest changes from the main branch.

Make sure to merge this creating a merge commit.

Do not squash-merge this PR. Do not rebase and merge.

…aging (#1122) Adds lineageFields to the backend config for all organisms that expose lineage/clade filters on the website. These fields are used by the backend to validate lineage filters in collection objects. Fields were identified in two ways: 1. Fetching `<lapis-url>/llms.txt` for each organism and extracting fields annotated as "(STRING, lineage index generated)" — these were found for covid, mpox, rsvA, rsvB, cchf, and denv1–4. 2. Reading the frontend view files (e.g. h5n1.ts, h3n2.ts) for organisms where llms.txt returned no lineage index fields but the website still exposes a variant/clade selector — covering h5n1, h1n1pdm, h3n2, influenzaA, influenzaB, victoria, westNile, and measles. Summary of lineageFields added per organism: - covid (staging only, prod already had it): pangoLineage, nextcladePangoLineage - h5n1: clade - h1n1pdm: cladeHA, cladeNA - h3n2: cladeHA, cladeNA - influenzaA: subtypeHA, subtypeNA - influenzaB: lineageHA - victoria: cladeHA, cladeNA - mpox: lineage, clade - westNile: lineage - rsvA: lineage - rsvB: lineage - cchf: lineage_S - denv1–4: clade - measles: genotype Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

vercel · 2026-04-08T11:43:18Z

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Project	Deployment	Actions	Updated (UTC)
dashboards	Ready	Preview, Comment	Apr 21, 2026 7:28am

Bumps [lewagon/wait-on-check-action](https://github.com/lewagon/wait-on-check-action) from 1.6.0 to 1.6.1. - [Release notes](https://github.com/lewagon/wait-on-check-action/releases) - [Changelog](https://github.com/lewagon/wait-on-check-action/blob/master/CHANGELOG.md) - [Commits](lewagon/wait-on-check-action@v1.6.0...v1.6.1) --- updated-dependencies: - dependency-name: lewagon/wait-on-check-action dependency-version: 1.6.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…1104) Bumps [org.jetbrains.exposed:exposed-json](https://github.com/JetBrains/Exposed) from 0.56.0 to 1.1.1. - [Release notes](https://github.com/JetBrains/Exposed/releases) - [Changelog](https://github.com/JetBrains/Exposed/blob/main/CHANGELOG.md) - [Commits](JetBrains/Exposed@0.56.0...1.1.1) --- updated-dependencies: - dependency-name: org.jetbrains.exposed:exposed-json dependency-version: 1.1.1 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* foO * fix import

* feat(website): disable collections for Influenza A and B Add hasCollections flag to organismConfig to control whether an organism appears in the collections menu and overview page. Set to false for influenzaA and influenzaB which don't have collections support. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * preserve supplementary separator * Make the 'has collections' switch part of the application config, enforce in backend. * tests * weird type stuff * address review --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

…tions and variants tables (#1119) * feat(collections): add created_at and updated_at timestamps to collections and variants tables Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * feat(collections): expose createdAt and updatedAt in API responses Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * test(collections): add timestamp tests and fix Jackson Instant deserialization Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * test(collections): reject client-provided timestamp fields with 400 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix(collections): truncate timestamps to milliseconds to avoid precision mismatches Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * pass in 'now' * truncate backfill timestamps * post-rebase fixes --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

* 1120 upload gradle test report * 1120 revert failing test * 1120 only upload on failure

…14 updates (#1139) * chore(website): bump the minorandpatch group across 1 directory with 14 updates Bumps the minorandpatch group with 13 updates in the /website directory: | Package | From | To | | --- | --- | --- | | [@tanstack/react-query](https://github.com/TanStack/query/tree/HEAD/packages/react-query) | `5.95.2` | `5.99.0` | | [axios](https://github.com/axios/axios) | `1.14.0` | `1.15.0` | | [katex](https://github.com/KaTeX/KaTeX) | `0.16.44` | `0.16.45` | | [react](https://github.com/facebook/react/tree/HEAD/packages/react) | `19.2.4` | `19.2.5` | | [react-dom](https://github.com/facebook/react/tree/HEAD/packages/react-dom) | `19.2.4` | `19.2.5` | | [@playwright/test](https://github.com/microsoft/playwright) | `1.58.2` | `1.59.1` | | [@tanstack/eslint-plugin-query](https://github.com/TanStack/query/tree/HEAD/packages/eslint-plugin-query) | `5.95.2` | `5.99.0` | | [@typescript-eslint/eslint-plugin](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/eslint-plugin) | `8.58.0` | `8.58.2` | | [@typescript-eslint/parser](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/parser) | `8.58.0` | `8.58.2` | | [eslint-plugin-astro](https://github.com/ota-meshi/eslint-plugin-astro) | `1.6.0` | `1.7.0` | | [msw](https://github.com/mswjs/msw) | `2.12.14` | `2.13.2` | | [prettier](https://github.com/prettier/prettier) | `3.8.1` | `3.8.2` | | [typescript-eslint](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/typescript-eslint) | `8.58.0` | `8.58.2` | Updates `@tanstack/react-query` from 5.95.2 to 5.99.0 - [Release notes](https://github.com/TanStack/query/releases) - [Changelog](https://github.com/TanStack/query/blob/main/packages/react-query/CHANGELOG.md) - [Commits](https://github.com/TanStack/query/commits/@tanstack/react-query@5.99.0/packages/react-query) Updates `axios` from 1.14.0 to 1.15.0 - [Release notes](https://github.com/axios/axios/releases) - [Changelog](https://github.com/axios/axios/blob/v1.x/CHANGELOG.md) - [Commits](axios/axios@v1.14.0...v1.15.0) Updates `katex` from 0.16.44 to 0.16.45 - [Release notes](https://github.com/KaTeX/KaTeX/releases) - [Changelog](https://github.com/KaTeX/KaTeX/blob/main/CHANGELOG.md) - [Commits](KaTeX/KaTeX@v0.16.44...v0.16.45) Updates `react` from 19.2.4 to 19.2.5 - [Release notes](https://github.com/facebook/react/releases) - [Changelog](https://github.com/facebook/react/blob/main/CHANGELOG.md) - [Commits](https://github.com/facebook/react/commits/v19.2.5/packages/react) Updates `react-dom` from 19.2.4 to 19.2.5 - [Release notes](https://github.com/facebook/react/releases) - [Changelog](https://github.com/facebook/react/blob/main/CHANGELOG.md) - [Commits](https://github.com/facebook/react/commits/v19.2.5/packages/react-dom) Updates `@playwright/test` from 1.58.2 to 1.59.1 - [Release notes](https://github.com/microsoft/playwright/releases) - [Commits](microsoft/playwright@v1.58.2...v1.59.1) Updates `@tanstack/eslint-plugin-query` from 5.95.2 to 5.99.0 - [Release notes](https://github.com/TanStack/query/releases) - [Changelog](https://github.com/TanStack/query/blob/main/packages/eslint-plugin-query/CHANGELOG.md) - [Commits](https://github.com/TanStack/query/commits/@tanstack/eslint-plugin-query@5.99.0/packages/eslint-plugin-query) Updates `@typescript-eslint/eslint-plugin` from 8.58.0 to 8.58.2 - [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/v8.58.2/packages/eslint-plugin) Updates `@typescript-eslint/parser` from 8.58.0 to 8.58.2 - [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/v8.58.2/packages/parser) Updates `eslint-plugin-astro` from 1.6.0 to 1.7.0 - [Release notes](https://github.com/ota-meshi/eslint-plugin-astro/releases) - [Changelog](https://github.com/ota-meshi/eslint-plugin-astro/blob/main/CHANGELOG.md) - [Commits](ota-meshi/eslint-plugin-astro@v1.6.0...v1.7.0) Updates `msw` from 2.12.14 to 2.13.2 - [Release notes](https://github.com/mswjs/msw/releases) - [Changelog](https://github.com/mswjs/msw/blob/main/CHANGELOG.md) - [Commits](mswjs/msw@v2.12.14...v2.13.2) Updates `playwright` from 1.58.2 to 1.59.1 - [Release notes](https://github.com/microsoft/playwright/releases) - [Commits](microsoft/playwright@v1.58.2...v1.59.1) Updates `prettier` from 3.8.1 to 3.8.2 - [Release notes](https://github.com/prettier/prettier/releases) - [Changelog](https://github.com/prettier/prettier/blob/main/CHANGELOG.md) - [Commits](prettier/prettier@3.8.1...3.8.2) Updates `typescript-eslint` from 8.58.0 to 8.58.2 - [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases) - [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/typescript-eslint/CHANGELOG.md) - [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v8.58.2/packages/typescript-eslint) --- updated-dependencies: - dependency-name: "@tanstack/react-query" dependency-version: 5.99.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: axios dependency-version: 1.15.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: katex dependency-version: 0.16.45 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: react dependency-version: 19.2.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: react-dom dependency-version: 19.2.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: "@playwright/test" dependency-version: 1.59.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@tanstack/eslint-plugin-query" dependency-version: 5.99.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: "@typescript-eslint/eslint-plugin" dependency-version: 8.58.2 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: "@typescript-eslint/parser" dependency-version: 8.58.2 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: eslint-plugin-astro dependency-version: 1.7.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: msw dependency-version: 2.13.2 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: playwright dependency-version: 1.59.1 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: minorandpatch - dependency-name: prettier dependency-version: 3.8.2 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: minorandpatch - dependency-name: typescript-eslint dependency-version: 8.58.2 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: minorandpatch ... Signed-off-by: dependabot[bot] <support@github.com> * fix(website): fix lint errors introduced by eslint-plugin upgrade Agent-Logs-Url: https://github.com/GenSpectrum/dashboards/sessions/0ab1242c-dcd7-4fba-b03e-90b52898562c Co-authored-by: fengelniederhammer <92720311+fengelniederhammer@users.noreply.github.com> * fix(website): fix browser test isolation for msw 2.13.x by using file-scoped worker fixture Agent-Logs-Url: https://github.com/GenSpectrum/dashboards/sessions/0ab1242c-dcd7-4fba-b03e-90b52898562c Co-authored-by: fengelniederhammer <92720311+fengelniederhammer@users.noreply.github.com> * format * fix types * fix import * put it in "finally" --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: fengelniederhammer <92720311+fengelniederhammer@users.noreply.github.com> Co-authored-by: Fabian Engelniederhammer <fabian.engelniederhammer@tngtech.com>

* docs: add AGENTS.md files * format * Update website/AGENTS.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update backend/AGENTS.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* test(website): add e2e test for single variant page * 1089 format * 1089 choose the correct lineage option (not the one in the collections thingy)

fhennig · 2026-04-21T11:56:12Z

Playwright tests failed once, I'm re-running them now. Failure:

Slow test file: [webkit] › tests/compareSideBySide.spec.ts (7.1m)
  Consider running tests from slow files in parallel. See: https://playwright.dev/docs/test-parallel
  1 failed
    [firefox] › tests/compareSideBySide.spec.ts:9:9 › The Compare Side-By-Side page › should show diagrams after selecting a variant in both columns - mpox 
  1 flaky
    [webkit] › tests/singleVariant.spec.ts:9:9 › The Single Variant page › should show diagrams after selecting a variant - covid 
  335 passed (40.2m)

Edit - Update: Now other tests failed:

  1 failed
    [webkit] › tests/compareSideBySide.spec.ts:9:9 › The Compare Side-By-Side page › should show diagrams after selecting a variant in both columns - h5n1 
  3 flaky
    [firefox] › tests/compareSideBySide.spec.ts:9:9 › The Compare Side-By-Side page › should show diagrams after selecting a variant in both columns - covid 
    [firefox] › tests/sequencingEfforts.spec.ts:31:13 › The Sequencing Efforts Page › ebolaZaire › should allow selecting location and date range and then show diagrams 
    [webkit] › tests/compareSideBySide.spec.ts:9:9 › The Compare Side-By-Side page › should show diagrams after selecting a variant in both columns - h1n1pdm 
  333 passed (42.8m)

It's just being flaky - not great but I think we can move ahead with the merge.

vercel Bot deployed to Production April 8, 2026 11:43 View deployment

chore(backend): update exposed 0.56 -> 1.1.1 (#1127)

add18a5

vercel Bot deployed to Production April 10, 2026 07:16 View deployment

vercel Bot deployed to Production April 10, 2026 08:41 View deployment

vercel Bot deployed to Production April 10, 2026 09:47 View deployment

docs(backend): document auth handling in README (#1135)

8325216

vercel Bot deployed to Production April 13, 2026 07:16 View deployment

test(backend): check if Docker is up before running tests (#1132)

4617108

* foO * fix import

vercel Bot deployed to Production April 13, 2026 07:17 View deployment

vercel Bot deployed to Production April 15, 2026 13:38 View deployment

vercel Bot deployed to Production April 15, 2026 13:43 View deployment

chore(backend): bump Spring 3.4 -> 3.5 (#1141)

42fb2ab

vercel Bot deployed to Production April 15, 2026 13:50 View deployment

ci(backend): upload gradle test report when unit tests fail (#1140)

087dc16

* 1120 upload gradle test report * 1120 revert failing test * 1120 only upload on failure

vercel Bot deployed to Production April 16, 2026 07:25 View deployment

vercel Bot deployed to Production April 16, 2026 08:00 View deployment

vercel Bot deployed to Production April 20, 2026 06:03 View deployment

feat(website): enable RSV-B wastewater dashboard on prod (#1143)

c0f45eb

vercel Bot deployed to Production April 21, 2026 06:59 View deployment

test(website): add e2e test for single variant page (#1146)

376b393

* test(website): add e2e test for single variant page * 1089 format * 1089 choose the correct lineage option (not the one in the collections thingy)

vercel Bot deployed to Production April 21, 2026 07:28 View deployment

fhennig merged commit 31c7b85 into prod Apr 21, 2026
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chore: update prod from main - #1133

chore: update prod from main#1133
fhennig merged 14 commits into
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github-actions Bot commented Apr 8, 2026

Make sure to merge this creating a merge commit.

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vercel Bot commented Apr 8, 2026 •

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