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* feat(example-data): add Python pango lineage collection seeder
Adds example-data/lineages/seed.py, a Python script that fetches pango
lineage definitions from the upstream summary JSON and creates one
backend collection per lineage (nucleotide substitutions as variants).
Mirrors the patterns of seed.mjs: idempotent, supports --wait,
--url, --user-id, and --limit (default 10 for testing, 0 for all).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* feat(example-data): add requirements.txt and Dockerfile for lineages seeder
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(example-data): unified Python seeder with source modules
Replaces the split JS/Python approach with a single Python codebase:
- seed.py: main entry point with argparse subcommands
(covid-resistance-mutations, covid-pango-lineages)
- backend.py: shared BackendClient (wait, fetch, create)
- sources/resistance_mutations.py: port of seed.mjs resistance data
- sources/pango_lineages.py: pango lineage fetcher
- Dockerfile updated to run python3 seed.py
Running without a subcommand seeds all sources. --limit only applies
to the covid-pango-lineages subcommand (default: 10, 0 = all).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* feat(example-data): replace requirements.txt with pixi
- pixi.toml with [workspace] config, python 3.13, requests via PyPI
- pixi.lock committed for reproducibility
- Dockerfile updated to multi-stage: pixi builder copies site-packages
into python:3.13-slim final image
- Defines tasks: seed, seed-lineages, seed-all-lineages, seed-resistance
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* feat(example-data): upsert seed user via POST /users/sync before seeding
BackendClient now calls POST /users/sync (githubId=9999999999,
name="GenSpectrum Team") to obtain the internal user id before any
collection API calls. wait_for_backend() uses this call for polling.
Removes the --user-id CLI flag.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* chore: add Python and pixi entries to .gitignore
* docs(example-data): update README for Python/pixi seeder
* feat(example-data): upsert collections instead of skipping existing ones
Collections are now always created or updated (matched by name).
Adds BackendClient.update_collection() using PUT /collections/{id}.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* test(example-data): add test suite with mock source and mocked HTTP backend
38 tests across 4 files:
- test_backend.py: BackendClient (responses library for HTTP mocking)
- test_resistance_mutations.py: mature_name offset math, collection structure
- test_pango_lineages.py: collection building, variant filtering, HTTP fetch
- test_seed.py: seed_source create/update/mixed upsert logic
Run with: pixi run -e test test
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* chore: rename example-data to collection-seeding
* fix(ci): update example-data path to collection-seeding, remove unused SEED_USER_ID
* fix(collection-seeding): use genspectrum-bot GitHub ID (218605180) for user sync
* refactor(collection-seeding): add TypedDict types (Collection, Variant, FilterObject, ExistingCollection)
* refactor(collection-seeding): authenticate via API key through website proxy
Replace the /users/sync + userId query param approach with a pre-provisioned
API key sent as Authorization: Bearer. The seeder now talks to the website
proxy (/api/collections) instead of the backend directly, removing the need
for backend access inside docker-compose.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): rename backend.py to api.py, BackendClient to ApiClient
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): rename test_backend.py to test_api.py, document name-matching caveat
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* chore(collection-seeding): pin pixi dependencies, fix README default URL
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix(collection-seeding): fix Dockerfile COPY after backend.py→api.py rename, add missing models.py
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* feat(collection-seeding): add repeat loop via REPEAT_INTERVAL_HOURS env var, run every 8h in compose
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* docs(collection-seeding): document REPEAT_INTERVAL_HOURS in README
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): convert sources to classes with Source ABC
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* README
* refactor(collection-seeding): move _build_collection into class, default to no lineage limit, add sample task
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* docs(collection-seeding): add docstring to Source ABC
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): use None for no limit, move docstrings to classes, reorder resistance_mutations.py
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): move test collections out of MockSource into test_seed.py
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): --source flag, ALL_SOURCES registry, PangoLineagesSampleSource, --list command
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): move ALL_SOURCES to dedicated sources/registry.py
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): reorder seed.py with main first
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix(collection-seeding): don't require --api-key for --list
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): move repeat loop into main(), add --repeat-interval-hours flag
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* docs(collection-seeding): update README with sample source, SEEDER_API_KEY, and new CLI flags
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix(collection-seeding): crash on error in repeat mode instead of swallowing
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* feat(collection-seeding): restructure pango lineage variants into 4 fixed types
Each collection now has exactly 4 variants (nucleotide substitutions,
amino acid substitutions, new nucleotide substitutions, new amino acid
substitutions) instead of one variant per individual nucleotide substitution.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix(collection-seeding): strip organism from PUT body to avoid 400
CollectionUpdate has no organism field and the backend is configured with
fail-on-unknown-properties=true, so including organism caused every update
to fail with a Bad Request.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): defer REPEAT_INTERVAL_HOURS parsing to argparse, remove seed.mjs
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* chore(collection-seeding): rename pixi workspace from example-data-seeder to collection-seeding
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): use dict literal instead of Collection() constructor in pango_lineages
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): make Source.name an abstract property to enforce subclass definition
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* chore(collection-seeding): add .dockerignore to exclude .pixi, tests, and docs from build context
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* chore(collection-seeding): add ruff for linting and formatting
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* chore(collection-seeding): use whitelist dockerignore with COPY . .
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* refactor(collection-seeding): raise RuntimeError instead of sys.exit in api.py
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* docs(collection-seeding): fix idempotency description in seed.py
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix(collection-seeding): convert REPEAT_INTERVAL_HOURS env var to float
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* docs: update collection-seeding ADR with Kotlin rationale
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* feat(collection-seeding): exclude sample source from default run
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* ci(collection-seeding): run Python tests before building Docker image
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix(docker-compose): hardcode dummy system user API key for both backend and seeder
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* fix(ci): set manifest-path for setup-pixi in seeder workflow
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* feat(collection-seeding): add searchable tags to collection descriptions
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* feat(collection-seeding): detect and delete orphaned pango lineage collections
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* Potential fix for pull request finding
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
* Update docs/arc42/09-architecture-decisions.md
Co-authored-by: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com>
---------
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com>
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* feat(backend): add excludeSystemCollections param to GET /collections Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * feat(website): exclude system collections from collections overview table Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix(website): update CollectionsOverview test mock to expect excludeSystemCollections param Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * test(backend): add tests for excludeSystemCollections param on GET /collections Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix * Change system user ID handling * refactor(backend): make systemUserId cache thread-safe with @volatile Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * refactor(test): make excludeSystemCollections optional in mockGetCollectionSummaries The helper was silently asserting excludeSystemCollections='true' on every call, making the signature misleading and preventing tests from asserting the param is absent or false. It now only asserts the param when explicitly provided, and existing browser-spec callers are updated to pass true explicitly. Also renames a backend test to follow the GIVEN/WHEN/THEN convention. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * docs(backend): document excludeSystemCollections param in CollectionsController @operation Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * refactor(website): simplify getCollectionSummaries by passing params object directly Widen EndpointParameters.requestParams to accept string | boolean | undefined so axios handles serialization natively, eliminating manual param assembly. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * refactor(website): remove unused BackendApiRouteMocker.mockGetCollectionSummaries Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * format --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Removes the isStaging() gates that were redirecting to 404 and hiding the Collections menu entries outside of staging. Closes #1108 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.