feat: Gene Info Endpoint#756
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- Add `src/mavedb/lib/hgnc/client.py` with `fetch_gene_info()` that queries the HGNC REST API and returns a `HGNCGeneInfo` dataclass (symbol, name, hgnc_id, locus_group, location, omim_id) - Add `HGNCGeneNotFoundError` and `HGNCServiceError` domain exceptions to `lib/exceptions.py` - Add `HGNC_REST_BASE_URL` constant and package `__init__` files - Add unit and network integration tests for the new client
- Add `GET /genes/{symbol}` router that fetches HGNC gene identity
and returns paginated published score sets targeting that gene
- Add `GeneResponse` view model with gene metadata and score set
pagination fields (limit, offset, total, total_scored_variants)
- Register the genes router in `server_main.py`
- Add `GeneSymbolConverter` for URL path parameter validation
- Add router tests covering happy path and error cases
Add `pytest.importorskip("starlette")` guard to both HGNC client test
files, since the logging context module depends on starlette and would
cause an ImportError in environments where starlette is absent.
5 tasks
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API support for VariantEffect/mavedb-ui#682
This pull request introduces a new
/genes/{symbol}API endpoint that provides gene identity and associated published score sets using data from the HGNC REST API. The implementation includes robust error handling, a new client for interacting with HGNC, and comprehensive tests to ensure reliability and correct behavior.Major features and changes:
New gene endpoint and API integration
src/mavedb/routers/genes.py) that exposes a/genes/{symbol}endpoint. This endpoint fetches gene information from the HGNC REST API and returns it along with associated public score sets, supporting pagination and error handling.GeneResponseinsrc/mavedb/view_models/gene.pyto structure the gene data and associated score sets returned by the endpoint.src/mavedb/server_main.py). [1] [2] [3]HGNC REST client and error handling
src/mavedb/lib/hgnc/client.pyto fetch and validate gene information, with custom exceptions for not found and service errors.HGNCGeneNotFoundErrorandHGNCServiceErrorinsrc/mavedb/lib/exceptions.pyfor precise error reporting.Configuration and constants
HGNC_REST_BASE_URLconstant to centralize the HGNC API base URL.Testing
tests/lib/hgnc/test_hgnc_client.py) and network tests (tests/lib/hgnc/network/test_hgnc_client.py) to cover the new client’s behavior, including error cases and integration with the live HGNC REST API. [1] [2]These changes together enable robust, production-ready gene lookup and score set retrieval by symbol, backed by HGNC’s authoritative gene data and integrated with MaveDB’s public score set system.