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Generalized collections UI#1077

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fhennig wants to merge 34 commits intogeneralized-collections-frontend-apifrom
generalized-collections-ui
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Generalized collections UI#1077
fhennig wants to merge 34 commits intogeneralized-collections-frontend-apifrom
generalized-collections-ui

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@fhennig fhennig commented Mar 16, 2026 •
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resolves #

Summary

  • src/backendApi/ — moved from src/components/subscriptions/backendApi/ to sit alongside
    src/lapis/ and src/covspectrum/; shared backend proxy logic extracted so collections and
    subscriptions routes share a single implementation
  • New Zod schemas in src/types/Collection.ts for response, request, and update types, following
    the same pattern as subscriptions
  • 5 new backend service methods: getCollections, getCollection, postCollection, putCollection,
    deleteCollection
  • New pages under /collections/[organism]/:
    • Hub page listing all organisms
    • Overview table (ID, name, description, variant count) with row links
    • Detail view (collection metadata + per-variant cards with type badge and field display)
    • Create form
    • Edit form (pre-populated from fetched collection, preserves variant IDs for update)
  • Shared CollectionForm component used by both create and edit, with a VariantEditor supporting
    both query-type (LAPIS filter expressions) and mutation-list-type variants

Screenshot

PR Checklist

  • All necessary documentation has been adapted.
  • The implemented feature is covered by an appropriate test.

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vercel bot commented Mar 16, 2026 •
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dashboards Ready Ready Preview, Comment Mar 23, 2026 11:32am

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@fhennig fhennig changed the base branch from main to generalized-collections-pt1 March 16, 2026 12:50
@fhennig fhennig force-pushed the generalized-collections-ui branch from 9bf63dc to 760f283 Compare March 17, 2026 09:30
@fhennig fhennig force-pushed the generalized-collections-ui branch from 760f283 to db49022 Compare March 17, 2026 10:11
@fhennig fhennig self-assigned this Mar 17, 2026
@fhennig fhennig changed the base branch from generalized-collections-pt1 to generalized-collections-frontend-api March 17, 2026 10:16
@fhennig fhennig force-pushed the generalized-collections-frontend-api branch from 6ff08e9 to 8ca09af Compare March 17, 2026 15:04
@fhennig fhennig force-pushed the generalized-collections-ui branch from db49022 to ce8db16 Compare March 17, 2026 15:06
@fhennig fhennig force-pushed the generalized-collections-frontend-api branch 2 times, most recently from 9e5ed16 to db7b941 Compare March 18, 2026 14:11
@fhennig fhennig force-pushed the generalized-collections-ui branch from ce8db16 to 74a1a44 Compare March 18, 2026 14:13
fhennig and others added 7 commits March 19, 2026 16:28
@fhennig @claude
Move backendApi to src/ top level alongside lapis and covspectrum
44ea0fb 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Add collection types and backend service methods
8946b0a 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Change collection and variant IDs from String to number
3a58527 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig
format
c0b44d9
@fhennig @claude
Extract shared backend proxy, add collections proxy route
71d5bd4 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Drop redundant userId args from collection service methods
0c5151f 
userId is injected by the backend proxy from the session, so there
is no need to pass it from the client.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Drop userId from subscription call sites
d2ac8c0 
The userId is added by the backend proxy, so callers don't need to supply it.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig fhennig force-pushed the generalized-collections-frontend-api branch from db7b941 to 9870dc4 Compare March 19, 2026 15:28
fhennig and others added 23 commits March 23, 2026 10:15
@fhennig @claude
fix(backend): rename MutationListDefinition to FilterObject (#1095)
83164e6 
* Rename MutationListDefinition to FilterObject

- MutationListDefinition → FilterObject
- MutationListVariantType → FilterObjectVariantType
- MUTATION_LIST → FILTER_OBJECT (enum values and VariantType)
- JSON discriminator "mutationList" → "filterObject"
- Field mutationList → filterObject throughout
- DB column "mutation_list" → "filter_object", stored value updated

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* Spell out abbreviated field names in FilterObject

aa -> aminoAcid, nuc -> nucleotide:
- aaMutations -> aminoAcidMutations
- nucMutations -> nucleotideMutations
- aaInsertions -> aminoAcidInsertions
- nucInsertions -> nucleotideInsertions

Also fix missed .mutationList. -> .filterObject. accesses in tests.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* Convert FilterObject to regular class with JsonAnySetter for filters

- Remove data class; no-arg constructor, var properties
- Arbitrary extra JSON properties captured via @JsonAnySetter into a
  private map, exposed via @JsonAnyGetter (no longer a "filters" sub-object)
- Spell out field names: aa -> aminoAcid, nuc -> nucleotide
- Update all call sites to use .apply { } instead of constructor params
- Restructure FilterObjectTest: explicit JSON string comparisons,
  full and partial serialization/deserialization, and a type-error test

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* Update V1.1 migration: mutation_list -> filter_object, mutationList -> filterObject

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* Fix remaining mutationList -> filterObject in test JSON strings

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* Add equals/hashCode to FilterObject

Lost when converting from data class.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* Rename FilterObjectTest methods to WHEN/THEN convention

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* Use GIVEN/WHEN/THEN naming convention in FilterObjectTest

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* docs

* Rename MutationList* variant classes to FilterObject*

- MutationListVariant -> FilterObjectVariant
- MutationListVariantRequest -> FilterObjectVariantRequest
- MutationListVariantUpdate -> FilterObjectVariantUpdate
- Related local variables and test helpers updated

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* Add another test

---------

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Adapt Collection types to renamed FilterObject backend API
8194462 
- MutationListDefinition -> FilterObject
- mutationList discriminator -> filterObject
- mutationList field -> filterObject on variant objects
- aaMutations/nucMutations/aaInsertions/nucInsertions -> spelled-out names
- filters sub-object removed; arbitrary filter props now top-level via catchall

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Move backendProxy.ts from pages/api/ to backendApi/
b69b448 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Split collections catch-all route into explicit per-endpoint files
3bdec17 
Replaces [...path].ts with index.ts (GET+POST) and [id].ts (GET+PUT+DELETE),
making auth requirements per endpoint explicit. Also adds proxyToBackendOptionalAuth
to backendProxy.ts to support endpoints where auth is optional.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig
Add collection page stubs
4384ab0
@fhennig @claude
Add new collection form with variant editor
36798ec 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Add collections overview table
74cdd9c 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Add collection detail view
331faa5 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Extract shared CollectionForm, add edit form
6134f0c 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Add delete button to edit form, restrict edit button to collection owner
4b3dff7 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Fix linting and formatting issues
15224df 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Add Collections dropdown to nav, fix exclusive menu behavior
88470fe 
- Add Collections mega menu dropdown listing all organisms
- Use details[name] exclusive accordion to close sibling menus on open

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Use two-column layout for collection form general fields
9941db0 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Change collection and variant IDs from String to number
3c55bf1 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Fix edit button visibility by coercing GitHub user ID to string
e0d409a 
GitHub returns profile.id as a number, but the backend stores ownedBy
as a string. Strict equality between the two always returned false.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Polish collections overview and detail UI
3b48a5d 
- Use contents <a> for clickable rows with proper cursor
- Row hover uses bg-base-300 (distinct from zebra bg-base-200)
- Left-align ID and variant count column headers
- Show organism label in page headline
- Replace text-base-content opacity modifiers with explicit gray colors
- Show #<id> prefix in detail view headline
- Replace Details card with inline organism/owner sentence

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig
format
e519ddd
@fhennig @claude
Redesign collection form layout with 3-column grid and inline variant…
f3888a4 
… controls

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Thread DashboardsConfig through collection form and wrap with GsApp
81ec7bc 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Use GsMutationFilter for mutation list variants, fix SSR by switching…
ba61098 
… to client:only

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Redesign variant editor with thirds layout and expanding description …
b30c3b5 
…textarea

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig @claude
Add showLabel prop to GsMutationFilter, hide label in variant editor
fc2a759 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig
some more form improvements
902ea5e
@fhennig fhennig force-pushed the generalized-collections-ui branch from 63fa289 to 902ea5e Compare March 23, 2026 10:22
fhennig and others added 2 commits March 23, 2026 11:09
@fhennig @claude
Allow anonymous browsing of collections, hide create actions for unau…
53d4443 
…thenticated users

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@fhennig
Change menu
909df20
@fhennig fhennig force-pushed the generalized-collections-frontend-api branch from 3e567d5 to e951f78 Compare March 23, 2026 12:28
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