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… the page state (#1166) * 1156 vibe code * 1156 don't ignore lint * 1156 extract mutation * 1156 also commit the test * 1156 loading spinner * 1156 show when valid * 1156 add doFullValidation param to query endpoint * 1156 on error, also just show an icon * 1156 fix test * 1156 format * 1156 fix types * 1156 proper error tooltip * 1156 "sticky" tooltip * 1156 close sticky tooltip * 1156 extract component * 1156 do full validation * 1156 do todo * 1156 fix stuff * 1156 better test * 1156 type=button * 1156 relax assertion Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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* Fix auth secret regenerating on every server restart Remove hardcoded `crypto.randomUUID()` as the auth secret — auth-astro and @auth/core both automatically read AUTH_SECRET from the environment, so the explicit secret field was overriding that and causing all sessions to be invalidated on every restart/deploy. Add AUTH_SECRET to .env.example with generation instructions. Fixes #1145 * Add e2e test for auth session cookie Set a fixed AUTH_SECRET in docker-compose and .env.e2e so tests can mint valid session cookies with a known secret. Add a Playwright test that verifies the account icon appears (not the Login button) when an authenticated cookie is present — this also acts as a regression test for the secret-regenerating bug: if AUTH_SECRET were ignored, the minted cookie would fail to decode and the test would fail. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Add hover test for username in auth dropdown Extract cookie setup into a helper, add name to the minted token, and test that hovering the account icon shows the username from the session. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Refactor e2e test helpers into tests/helpers/ directory Move authHelper into tests/helpers/ alongside a new organisms.ts (split out from the old helpers.ts) so helper files are grouped together rather than living in feature directories. Add authenticatedPage fixture to e2e.fixture.ts so tests declare auth as a dependency instead of calling the helper imperatively. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Add collection create/edit/delete UI Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Use default button style for New collection button Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * foo * hot-fix an issue * Add lineage filter to variant editor Reads lineageFields from the per-organism LAPIS config and renders a GsLineageFilter for each field above the mutation filter. Values are stored as plain strings in filterObject. Also fixes the type toggle discriminator ('mutationList' → 'filterObject') and adds the showLabel prop to GsMutationFilter. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Redesign variant editor controls Move mutation filter to top with label re-enabled, lineage filters below. Replace radio type toggle with a checkbox at the bottom. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Rename checkbox label and remove coverage query from variant form Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Add some memoization and callback wrapping * Prevent expensive Gs* web components from re-rendering on variant name/description changes The variant editor contains GsMutationFilter and GsLineageFilter — web components from @genspectrum/dashboard-components that are expensive to render. Previously, typing in the variant name or description field caused these components to re-render on every keystroke, resulting in noticeable input lag. Root cause: React re-renders the entire component subtree whenever a parent re-renders. Typing a name called setVariants in CollectionForm, which re-rendered all VariantEditors, which re-rendered MutationListVariantFields, which re-rendered the Gs* web components — even though none of their data had changed. Fix applied in layers: 1. CollectionForm: wrapped addVariant, updateVariant, removeVariant in useCallback so their references are stable across re-renders. 2. VariantEditor: wrapped in memo so it only re-renders when its own props change, not when unrelated CollectionForm state (e.g. collection name) changes. The onChange/onRemove props are now stable thanks to (1), so memo's shallow comparison holds. 3. MutationListVariantFields: wrapped in memo and refactored to receive filterObject directly instead of the full variant object. This means its props only change when filter data changes — not when name or description changes. 4. handleFilterObjectChange: the onChange handler passed to MutationListVariantFields needs to build a full VariantUpdate including name and description. If we put variant in useCallback's deps, the callback is recreated on every name/description change, breaking memo. Instead, we store variant in a ref (variantRef.current = variant on every render) and read from it inside the callback. The ref is always current without being a dependency, so the callback is stable for the lifetime of the component. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * some rebase fixes * delete * undo * Polish collection edit/create UI - Add 'New collection' / 'Edit collection' page title - Use organism label in general info description - Make 'Add variant' button full-width - Default new variants to filterObject (unticked advanced query) - Fix bottom padding for both create and edit pages - Consistent label styles and textarea sizing throughout - Remove button styled for variant removal Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Add component and E2E tests for collection create/edit pages [WIP] Component tests (vitest-browser-react) for CollectionForm and VariantEditor are working. E2E tests for the create/edit pages are not yet fully working — the pages require authentication, which cannot be set up in tests until the AUTH_SECRET bug (random UUID on each server start) is fixed. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * docs * Add edit button to collection detail page for owners Shows an Edit button on the collection detail view only when the logged-in user is the owner. Fixes type mismatch between GitHub OAuth numeric user ID and the string ownedBy field by coercing with String() before comparing. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Add auth fixtures and unauthenticated access test for collection form Extract auth cookie setup into a shared authHelper, add authenticatedPage and authenticatedCollectionFormPage fixtures so tests declare auth as a dependency rather than calling a helper imperatively. Add a test verifying that the create collection page shows "Please login" when not authenticated. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Fix ownership check, error message, and clean up test files - Check server-side that the logged-in user owns the collection before rendering the edit page; redirect to /404 otherwise, matching the pattern used in the detail page - Fix inconsistent delete error message in CollectionEdit ("Failed to delete" → "Failed to delete collection") - Remove leftover auth/authHelper.ts and its duplicate import in e2e.fixture.ts - Remove E2E_test_notes.md Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Fix TypeScript errors in Inset and CollectionForm Restore PropsWithChildren<WithClassName> in Inset (matching the pattern used elsewhere) after the formatter incorrectly removed the type argument. Add `as const` to filterObject type literals in CollectionForm so TypeScript narrows them to the required literal type. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Revert accidental XFG* change in wastewaterConfig Restore A.D.1* as the default variant for the second wastewater config entry — XFG* was already set on the first entry and should not have been duplicated here. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Revert unused showLabel prop from GsMutationFilter The prop was added but never passed by any call site. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Use stable clientKey instead of index for variant list keys key={index} causes React to reuse component state from the wrong row when a variant is removed. Use variant.id when available (existing variants) or crypto.randomUUID() for new ones, preserved through updates. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Use named checkbox selector in CollectionFormPage Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Use named checkbox selector in VariantEditor browser spec Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Use named checkbox selector in CollectionForm browser spec Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Pass collection from edit.astro to CollectionEdit, avoiding duplicate fetch The page already fetches the collection for ownership validation, so passing it as a prop removes the redundant useQuery in CollectionEdit. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * refactor(website): move String cast for GitHub user ID to assignment site Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * refactor(website): extract DeleteCollectionSection from CollectionEdit Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix * fix * feat(website): redirect to new collection after creation Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * test(website): add E2E tests for create redirect and description deletion Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
* feat(example-data): add staging example data seeder Adds a new example-data/ folder with a Node.js script and Dockerfile that seed the backend with resistance mutation collections (3CLpro, RdRp, Spike mAb) on staging. The seeder runs as a Docker Compose service activated via --profile staging and is idempotent. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * feat(example-data): add CLI interface to seed.js Adds util.parseArgs-based CLI (no dependencies) with --url, --user-id, --session-token, --wait, and --help flags. Session token mode hits the website proxy at /api/collections with the correct cookie, mirroring the shell script. The wait retry loop auto-enables when no TTY is detected so Docker Compose behaviour is unchanged. Also adds a README with usage examples. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix(example-data): rename seed.js to .mjs, bump node to 25-alpine, always run seeder - Rename seed.js → seed.mjs to reflect ES module usage - Update Dockerfile to node:25-alpine - Remove `profiles: staging` from docker-compose so the seeder always runs - Update README accordingly Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix(example-data): remove session token support from seed.mjs Always call the backend directly; the session token path via the website proxy is no longer needed. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * feat(example-data): add CI workflow and publish seeder as Docker image - Add GitHub Actions workflow to build and push the seeder image to ghcr.io - Switch docker-compose to use the published image via SEEDER_TAG - Update README accordingly Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * update readme * seeder tag * node 24 --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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This pull request updates the
prodbranch with the latest changes from themainbranch.Make sure to merge this creating a merge commit.
Do not squash-merge this PR. Do not rebase and merge.