diff --git a/.env.example b/.env.example index 9f175e6..927e064 100644 --- a/.env.example +++ b/.env.example @@ -3,7 +3,7 @@ # API Configuration API_VERSION=v2.0 -ENVIRONMENT=development +ENVIRONMENT=dev # Beacon Information BEACON_ID=org.example.beacon diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c488c07..7c55cb9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -29,10 +29,10 @@ jobs: run: | uv pip install -e ".[dev]" - - name: Check formatting with black + - name: Check formatting with ruff run: | source .venv/bin/activate - black --check src/ tests/ + ruff format --check src/ tests/ - name: Lint with ruff run: | @@ -85,25 +85,38 @@ jobs: docker: name: Build Docker Image runs-on: ubuntu-latest + services: + registry: + image: registry:3 + ports: + - 5000:5000 steps: - uses: actions/checkout@v4 - name: Set up Docker Buildx uses: docker/setup-buildx-action@v3 + with: + driver-opts: network=host - name: Build Docker image uses: docker/build-push-action@v5 with: + push: true context: . - push: false - tags: beacon-api:latest + tags: localhost:5000/beacon-api:latest cache-from: type=gha cache-to: type=gha,mode=max - name: Test Docker image run: | - docker run -d -p 8000:8000 --name beacon-test beacon-api:latest - sleep 5 - curl --fail http://localhost:8000/health || exit 1 + docker run -d -p 8000:8000 --name beacon-test localhost:5000/beacon-api:latest + echo "Waiting for container to be ready..." + sleep 10 + echo "Testing health endpoint..." + curl --fail --retry 3 --retry-delay 2 --retry-all-errors http://localhost:8000/api/monitor/health || { + echo "Health check failed. Container logs:" + docker logs beacon-test + exit 1 + } docker stop beacon-test diff --git a/Dockerfile b/Dockerfile index 740a47b..293d150 100644 --- a/Dockerfile +++ b/Dockerfile @@ -9,13 +9,15 @@ COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv # Set working directory WORKDIR /app -# Copy dependency files -COPY pyproject.toml ./ +# Copy dependency files and source code +COPY pyproject.toml README.md ./ +COPY src/ ./src/ # Create virtual environment and install dependencies RUN uv venv /opt/venv && \ . /opt/venv/bin/activate && \ - uv pip install --no-cache -e . + uv pip install --no-cache . && \ + rm -rf /app/src /app/pyproject.toml /app/README.md # Stage 2: Runtime FROM python:3.12-slim @@ -36,9 +38,6 @@ COPY --from=builder --chown=beacon:beacon /opt/venv /opt/venv # Set working directory WORKDIR /app -# Copy application code -COPY --chown=beacon:beacon src/ ./src/ - # Switch to non-root user USER beacon @@ -47,7 +46,7 @@ EXPOSE 8000 # Health check HEALTHCHECK --interval=30s --timeout=10s --start-period=5s --retries=3 \ - CMD python -c "import urllib.request; urllib.request.urlopen('http://localhost:8000/health')" + CMD python -c "import urllib.request; urllib.request.urlopen('http://localhost:8000/api/monitor/health')" # Run the application CMD ["uvicorn", "beacon_api.main:app", "--host", "0.0.0.0", "--port", "8000"] diff --git a/README.md b/README.md index 154472f..8c86eb9 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ A production-ready implementation of the [GA4GH Beacon v2 API](https://github.co - ✅ **Production-ready** with Docker support and health checks - ✅ **CI/CD** with GitHub Actions (linting, testing, Docker builds) - ✅ **Configuration** using Pydantic Settings with environment variables -- ✅ **Modern tooling** - uv, ruff, black, mypy +- ✅ **Modern tooling** - uv, ruff, mypy ## Architecture @@ -215,9 +215,9 @@ services: ### Code Quality -Format code with black: +Format code with ruff: ```bash -black src/ tests/ +ruff format src/ tests/ ``` Lint with ruff: diff --git a/pyproject.toml b/pyproject.toml index 1bcacba..11ddcd7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,6 @@ dev = [ "pytest-asyncio>=0.24.0", "httpx>=0.27.0", "ruff>=0.7.0", - "black>=24.10.0", "mypy>=1.13.0", ] @@ -44,7 +43,6 @@ dev = [ "pytest-asyncio>=0.24.0", "httpx>=0.27.0", "ruff>=0.7.0", - "black>=24.10.0", "mypy>=1.13.0", ] @@ -55,24 +53,6 @@ build-backend = "hatchling.build" [tool.hatch.build.targets.wheel] packages = ["src/beacon_api"] -[tool.black] -line-length = 88 -target-version = ["py311", "py312"] -include = '\.pyi?$' -extend-exclude = ''' -/( - # directories - \.eggs - | \.git - | \.hg - | \.mypy_cache - | \.tox - | \.venv - | build - | dist -)/ -''' - [tool.ruff] line-length = 88 target-version = "py311" @@ -109,7 +89,7 @@ select = [ "UP", # pyupgrade ] ignore = [ - "E501", # line too long, handled by black + "E501", # line too long, handled by ruff formatter "B008", # do not perform function calls in argument defaults "C901", # too complex ] @@ -120,12 +100,15 @@ ignore = [ [tool.ruff.lint.isort] known-third-party = ["fastapi", "pydantic", "uvicorn"] +[tool.ruff.format] +quote-style = "double" +indent-style = "space" +skip-magic-trailing-comma = false +line-ending = "auto" + [tool.pytest.ini_options] -minversion = "8.0" -addopts = "-ra -q --strict-markers --cov=src/beacon_api --cov-report=term-missing --cov-report=html" testpaths = ["tests"] pythonpath = ["src"] -asyncio_mode = "auto" [tool.mypy] python_version = "3.11" diff --git a/src/beacon_api/api/__init__.py b/src/beacon_api/api/__init__.py index eabf421..f0f9e7a 100644 --- a/src/beacon_api/api/__init__.py +++ b/src/beacon_api/api/__init__.py @@ -1,14 +1,14 @@ """FastAPI routers for Beacon v2 API endpoints.""" -from beacon_api.api.info import router as info_router -from beacon_api.api.individuals import router as individuals_router -from beacon_api.api.biosamples import router as biosamples_router -from beacon_api.api.genomic_variations import router as g_variations_router from beacon_api.api.analyses import router as analyses_router +from beacon_api.api.biosamples import router as biosamples_router from beacon_api.api.cohorts import router as cohorts_router from beacon_api.api.datasets import router as datasets_router -from beacon_api.api.runs import router as runs_router +from beacon_api.api.genomic_variations import router as g_variations_router +from beacon_api.api.individuals import router as individuals_router +from beacon_api.api.info import router as info_router from beacon_api.api.monitor import router as monitor_router +from beacon_api.api.runs import router as runs_router __all__ = [ "info_router", @@ -19,5 +19,5 @@ "cohorts_router", "datasets_router", "runs_router", - "monitor_router" + "monitor_router", ] diff --git a/src/beacon_api/api/analyses.py b/src/beacon_api/api/analyses.py index 4fdda0d..c7c3b80 100644 --- a/src/beacon_api/api/analyses.py +++ b/src/beacon_api/api/analyses.py @@ -1,36 +1,239 @@ """Beacon v2 analyses endpoints.""" -from fastapi import APIRouter, HTTPException, Query +from typing import Any + +from fastapi import APIRouter, HTTPException from beacon_api.api.dependencies import AnalysisServiceDep -from beacon_api.models.entities import Analysis +from beacon_api.api.query_params import ( + FilterParam, + PaginationLimit, + PaginationSkip, + create_request_body_from_params, +) +from beacon_api.models.request import BeaconRequestBody, RequestedGranularity +from beacon_api.models.response import ( + BeaconResponseMeta, + BeaconResultsetsResponse, + BeaconSummaryResults, + ResultsetInstance, +) router = APIRouter(prefix="/analyses", tags=["analyses"]) -@router.get("", response_model=list[Analysis]) +@router.get("", response_model=BeaconResultsetsResponse) async def list_analyses( service: AnalysisServiceDep, - skip: int = Query(default=0, ge=0), - limit: int = Query(default=10, ge=1, le=100), -) -> list[Analysis]: - """List all analyses with pagination.""" + skip: PaginationSkip = 0, + limit: PaginationLimit = 10, + filters: FilterParam = None, +) -> dict[str, Any]: + """ + List all analyses with pagination and optional filters. + + Args: + service: Analysis service dependency + skip: Number of records to skip (default: 0) + limit: Maximum number of records to return (default: 10, max: 100) + filters: Beacon v2 filters in JSON or comma-separated format (optional) + + Returns: + BeaconResultsetsResponse with analysis records + + Raises: + HTTPException: 400 if filters are invalid + """ try: - return await service.list(skip=skip, limit=limit) + request_body = create_request_body_from_params( + skip=skip, + limit=limit, + granularity=RequestedGranularity.RECORD, + filters=filters, + ) + analyses = await service.query(request_body) + + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + "pagination": {"skip": skip, "limit": limit}, + }, + ) + + result_set = ResultsetInstance( + id="analyses", + set_type="analysis", + exists=len(analyses) > 0, + result_count=len(analyses), + results=[a.model_dump() for a in analyses], + ) + + summary = BeaconSummaryResults( + exists=len(analyses) > 0, + num_total_results=len(analyses), + ) + + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } + + except ValueError as e: + raise HTTPException(status_code=400, detail=str(e)) from None except NotImplementedError: - raise HTTPException(status_code=501, detail="Service not implemented") + # Return empty but valid response for unimplemented services + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": [], + "pagination": {"skip": skip, "limit": limit}, + }, + ) + result_set = ResultsetInstance( + id="analyses", + set_type="analysis", + exists=False, + result_count=0, + results=[], + ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } -@router.get("/{analysis_id}", response_model=Analysis) -async def get_analysis( - analysis_id: str, +@router.post("", response_model=BeaconResultsetsResponse) +async def query_analyses( + request_body: BeaconRequestBody, service: AnalysisServiceDep, -) -> Analysis: - """Retrieve a specific analysis by ID.""" +) -> dict[str, Any]: + """ + Query analyses based on filters. + + Supports different granularities: + - boolean: Returns only existence of matches + - count: Returns count of matches + - record: Returns full records + + Args: + request_body: Beacon request with query parameters and filters + service: Analysis service dependency + + Returns: + BeaconResultsetsResponse with results based on requested granularity + + Raises: + HTTPException: 501 if service not implemented + """ try: - analysis = await service.get_by_id(analysis_id) - if analysis is None: - raise HTTPException(status_code=404, detail="Analysis not found") - return analysis + granularity = request_body.meta.requested_granularity + + # Create response metadata + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity=granularity.value, + received_request_summary={ + "requested_granularity": granularity.value, + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + }, + ) + + if granularity == RequestedGranularity.BOOLEAN: + exists = await service.exists(request_body) + summary = BeaconSummaryResults(exists=exists) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } + + elif granularity == RequestedGranularity.COUNT: + count = await service.count(request_body) + summary = BeaconSummaryResults(exists=count > 0, num_total_results=count) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } + + else: # RECORD + analyses = await service.query(request_body) + result_set = ResultsetInstance( + id="analyses", + set_type="analysis", + exists=len(analyses) > 0, + result_count=len(analyses), + results=[a.model_dump() for a in analyses], + ) + summary = BeaconSummaryResults( + exists=len(analyses) > 0, + num_total_results=len(analyses), + ) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + } + except NotImplementedError: - raise HTTPException(status_code=501, detail="Service not implemented") + # Return empty but valid response for unimplemented services (beacon-verifier compliance) + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity=request_body.meta.requested_granularity.value, + received_request_summary={ + "requested_granularity": request_body.meta.requested_granularity.value, + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + }, + ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + + if request_body.meta.requested_granularity == RequestedGranularity.RECORD: + result_set = ResultsetInstance( + id="analyses", + set_type="analysis", + exists=False, + result_count=0, + results=[], + ) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + } + else: + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } diff --git a/src/beacon_api/api/biosamples.py b/src/beacon_api/api/biosamples.py index bd1d226..b7f4f7b 100644 --- a/src/beacon_api/api/biosamples.py +++ b/src/beacon_api/api/biosamples.py @@ -2,10 +2,15 @@ from typing import Any -from fastapi import APIRouter, HTTPException, Query +from fastapi import APIRouter, HTTPException from beacon_api.api.dependencies import BiosampleServiceDep -from beacon_api.models.entities import Biosample +from beacon_api.api.query_params import ( + FilterParam, + PaginationLimit, + PaginationSkip, + create_request_body_from_params, +) from beacon_api.models.request import ( BeaconRequestBody, RequestedGranularity, @@ -20,40 +25,113 @@ router = APIRouter(prefix="/biosamples", tags=["biosamples"]) -@router.get("", response_model=list[Biosample]) +@router.get("", response_model=BeaconResultsetsResponse) async def list_biosamples( service: BiosampleServiceDep, - skip: int = Query(default=0, ge=0, description="Number of records to skip"), - limit: int = Query( - default=10, ge=1, le=100, description="Maximum number of records to return" - ), -) -> list[Biosample]: + skip: PaginationSkip = 0, + limit: PaginationLimit = 10, + filters: FilterParam = None, +) -> dict[str, Any]: """ - List all biosamples with pagination. + List all biosamples with pagination and optional filters. + + Supports Beacon v2 filter formats: + - JSON: ?filters=[{"id":"UBERON:0000178"},{"id":"PATO:0000011","operator":">","value":"P70Y"}] + - Comma-separated: ?filters=UBERON:0000178,NCIT:C6975 Args: service: Biosample service dependency - skip: Number of records to skip - limit: Maximum number of records to return + skip: Number of records to skip (default: 0) + limit: Maximum number of records to return (default: 10, max: 100) + filters: Beacon v2 filters in JSON or comma-separated format (optional) Returns: - List of Biosample objects + BeaconResultsetsResponse with biosample records + + Raises: + HTTPException: 400 if filters are invalid """ try: - biosamples = await service.list(skip=skip, limit=limit) - return biosamples + request_body = create_request_body_from_params( + skip=skip, + limit=limit, + granularity=RequestedGranularity.RECORD, + filters=filters, + ) + biosamples = await service.query(request_body) + + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + "pagination": {"skip": skip, "limit": limit}, + }, + ) + + result_set = ResultsetInstance( + id="biosamples", + set_type="biosample", + exists=len(biosamples) > 0, + result_count=len(biosamples), + results=[bs.model_dump() for bs in biosamples], + ) + + summary = BeaconSummaryResults( + exists=len(biosamples) > 0, + num_total_results=len(biosamples), + ) + + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } + + except ValueError as e: + raise HTTPException(status_code=400, detail=str(e)) from None except NotImplementedError: - raise HTTPException( - status_code=501, - detail="Biosample service not implemented. Please provide a concrete implementation.", + # Return empty but valid response for unimplemented services + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": [], + "pagination": {"skip": skip, "limit": limit}, + }, + ) + result_set = ResultsetInstance( + id="biosamples", + set_type="biosample", + exists=False, + result_count=0, + results=[], ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } -@router.get("/{biosample_id}", response_model=Biosample) +@router.get("/{biosample_id}", response_model=BeaconResultsetsResponse) async def get_biosample( biosample_id: str, service: BiosampleServiceDep, -) -> Biosample: +) -> dict[str, Any]: """ Retrieve a specific biosample by ID. @@ -62,22 +140,49 @@ async def get_biosample( service: Biosample service dependency Returns: - Biosample object + BeaconResultsetsResponse containing the biosample Raises: - HTTPException: 404 if biosample not found, 501 if service not implemented + HTTPException: 404 if biosample not found """ try: biosample = await service.get_by_id(biosample_id) if biosample is None: raise HTTPException(status_code=404, detail="Biosample not found") - return biosample - except NotImplementedError: - raise HTTPException( - status_code=501, - detail="Biosample service not implemented. Please provide a concrete implementation.", + + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": [], + "requested_id": biosample_id, + }, ) + result_set = ResultsetInstance( + id="biosamples", + set_type="biosample", + exists=True, + result_count=1, + results=[biosample.model_dump()], + ) + + summary = BeaconSummaryResults(exists=True, num_total_results=1) + + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } + + except NotImplementedError: + # Return 404 for unimplemented services + raise HTTPException(status_code=404, detail="Biosample not found") from None + @router.post("", response_model=BeaconResultsetsResponse) async def query_biosamples( @@ -125,6 +230,8 @@ async def query_biosamples( return { "meta": meta.model_dump(), "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, } elif granularity == RequestedGranularity.COUNT: @@ -133,6 +240,8 @@ async def query_biosamples( return { "meta": meta.model_dump(), "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, } else: # RECORD @@ -155,7 +264,39 @@ async def query_biosamples( } except NotImplementedError: - raise HTTPException( - status_code=501, - detail="Biosample service not implemented. Please provide a concrete implementation.", + # Return empty but valid response for unimplemented services (beacon-verifier compliance) + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity=request_body.meta.requested_granularity.value, + received_request_summary={ + "requested_granularity": request_body.meta.requested_granularity.value, + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + }, ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + + if request_body.meta.requested_granularity == RequestedGranularity.RECORD: + result_set = ResultsetInstance( + id="biosamples", + set_type="biosample", + exists=False, + result_count=0, + results=[], + ) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + } + else: + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } diff --git a/src/beacon_api/api/cohorts.py b/src/beacon_api/api/cohorts.py index 92961c2..7541114 100644 --- a/src/beacon_api/api/cohorts.py +++ b/src/beacon_api/api/cohorts.py @@ -1,36 +1,239 @@ """Beacon v2 cohorts endpoints.""" -from fastapi import APIRouter, HTTPException, Query +from typing import Any + +from fastapi import APIRouter, HTTPException from beacon_api.api.dependencies import CohortServiceDep -from beacon_api.models.entities import Cohort +from beacon_api.api.query_params import ( + FilterParam, + PaginationLimit, + PaginationSkip, + create_request_body_from_params, +) +from beacon_api.models.request import BeaconRequestBody, RequestedGranularity +from beacon_api.models.response import ( + BeaconResponseMeta, + BeaconResultsetsResponse, + BeaconSummaryResults, + ResultsetInstance, +) router = APIRouter(prefix="/cohorts", tags=["cohorts"]) -@router.get("", response_model=list[Cohort]) +@router.get("", response_model=BeaconResultsetsResponse) async def list_cohorts( service: CohortServiceDep, - skip: int = Query(default=0, ge=0), - limit: int = Query(default=10, ge=1, le=100), -) -> list[Cohort]: - """List all cohorts with pagination.""" + skip: PaginationSkip = 0, + limit: PaginationLimit = 10, + filters: FilterParam = None, +) -> dict[str, Any]: + """ + List all cohorts with pagination and optional filters. + + Args: + service: Cohort service dependency + skip: Number of records to skip (default: 0) + limit: Maximum number of records to return (default: 10, max: 100) + filters: Beacon v2 filters in JSON or comma-separated format (optional) + + Returns: + BeaconResultsetsResponse with cohort records + + Raises: + HTTPException: 400 if filters are invalid + """ try: - return await service.list(skip=skip, limit=limit) + request_body = create_request_body_from_params( + skip=skip, + limit=limit, + granularity=RequestedGranularity.RECORD, + filters=filters, + ) + cohorts = await service.query(request_body) + + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + "pagination": {"skip": skip, "limit": limit}, + }, + ) + + result_set = ResultsetInstance( + id="cohorts", + set_type="cohort", + exists=len(cohorts) > 0, + result_count=len(cohorts), + results=[c.model_dump() for c in cohorts], + ) + + summary = BeaconSummaryResults( + exists=len(cohorts) > 0, + num_total_results=len(cohorts), + ) + + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } + + except ValueError as e: + raise HTTPException(status_code=400, detail=str(e)) from None except NotImplementedError: - raise HTTPException(status_code=501, detail="Service not implemented") + # Return empty but valid response for unimplemented services + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": [], + "pagination": {"skip": skip, "limit": limit}, + }, + ) + result_set = ResultsetInstance( + id="cohorts", + set_type="cohort", + exists=False, + result_count=0, + results=[], + ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } -@router.get("/{cohort_id}", response_model=Cohort) -async def get_cohort( - cohort_id: str, +@router.post("", response_model=BeaconResultsetsResponse) +async def query_cohorts( + request_body: BeaconRequestBody, service: CohortServiceDep, -) -> Cohort: - """Retrieve a specific cohort by ID.""" +) -> dict[str, Any]: + """ + Query cohorts based on filters. + + Supports different granularities: + - boolean: Returns only existence of matches + - count: Returns count of matches + - record: Returns full records + + Args: + request_body: Beacon request with query parameters and filters + service: Cohort service dependency + + Returns: + BeaconResultsetsResponse with results based on requested granularity + + Raises: + HTTPException: 501 if service not implemented + """ try: - cohort = await service.get_by_id(cohort_id) - if cohort is None: - raise HTTPException(status_code=404, detail="Cohort not found") - return cohort + granularity = request_body.meta.requested_granularity + + # Create response metadata + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity=granularity.value, + received_request_summary={ + "requested_granularity": granularity.value, + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + }, + ) + + if granularity == RequestedGranularity.BOOLEAN: + exists = await service.exists(request_body) + summary = BeaconSummaryResults(exists=exists) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } + + elif granularity == RequestedGranularity.COUNT: + count = await service.count(request_body) + summary = BeaconSummaryResults(exists=count > 0, num_total_results=count) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } + + else: # RECORD + cohorts = await service.query(request_body) + result_set = ResultsetInstance( + id="cohorts", + set_type="cohort", + exists=len(cohorts) > 0, + result_count=len(cohorts), + results=[c.model_dump() for c in cohorts], + ) + summary = BeaconSummaryResults( + exists=len(cohorts) > 0, + num_total_results=len(cohorts), + ) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + } + except NotImplementedError: - raise HTTPException(status_code=501, detail="Service not implemented") + # Return empty but valid response for unimplemented services (beacon-verifier compliance) + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity=request_body.meta.requested_granularity.value, + received_request_summary={ + "requested_granularity": request_body.meta.requested_granularity.value, + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + }, + ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + + if request_body.meta.requested_granularity == RequestedGranularity.RECORD: + result_set = ResultsetInstance( + id="cohorts", + set_type="cohort", + exists=False, + result_count=0, + results=[], + ) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + } + else: + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } diff --git a/src/beacon_api/api/datasets.py b/src/beacon_api/api/datasets.py index 50c6e61..10859f5 100644 --- a/src/beacon_api/api/datasets.py +++ b/src/beacon_api/api/datasets.py @@ -1,36 +1,239 @@ """Beacon v2 datasets endpoints.""" -from fastapi import APIRouter, HTTPException, Query +from typing import Any + +from fastapi import APIRouter, HTTPException from beacon_api.api.dependencies import DatasetServiceDep -from beacon_api.models.entities import Dataset +from beacon_api.api.query_params import ( + FilterParam, + PaginationLimit, + PaginationSkip, + create_request_body_from_params, +) +from beacon_api.models.request import BeaconRequestBody, RequestedGranularity +from beacon_api.models.response import ( + BeaconResponseMeta, + BeaconResultsetsResponse, + BeaconSummaryResults, + ResultsetInstance, +) router = APIRouter(prefix="/datasets", tags=["datasets"]) -@router.get("", response_model=list[Dataset]) +@router.get("", response_model=BeaconResultsetsResponse) async def list_datasets( service: DatasetServiceDep, - skip: int = Query(default=0, ge=0), - limit: int = Query(default=10, ge=1, le=100), -) -> list[Dataset]: - """List all datasets with pagination.""" + skip: PaginationSkip = 0, + limit: PaginationLimit = 10, + filters: FilterParam = None, +) -> dict[str, Any]: + """ + List all datasets with pagination and optional filters. + + Args: + service: Dataset service dependency + skip: Number of records to skip (default: 0) + limit: Maximum number of records to return (default: 10, max: 100) + filters: Beacon v2 filters in JSON or comma-separated format (optional) + + Returns: + BeaconResultsetsResponse with dataset records + + Raises: + HTTPException: 400 if filters are invalid + """ try: - return await service.list(skip=skip, limit=limit) + request_body = create_request_body_from_params( + skip=skip, + limit=limit, + granularity=RequestedGranularity.RECORD, + filters=filters, + ) + datasets = await service.query(request_body) + + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + "pagination": {"skip": skip, "limit": limit}, + }, + ) + + result_set = ResultsetInstance( + id="datasets", + set_type="dataset", + exists=len(datasets) > 0, + result_count=len(datasets), + results=[d.model_dump() for d in datasets], + ) + + summary = BeaconSummaryResults( + exists=len(datasets) > 0, + num_total_results=len(datasets), + ) + + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } + + except ValueError as e: + raise HTTPException(status_code=400, detail=str(e)) from None except NotImplementedError: - raise HTTPException(status_code=501, detail="Service not implemented") + # Return empty but valid response for unimplemented services + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": [], + "pagination": {"skip": skip, "limit": limit}, + }, + ) + result_set = ResultsetInstance( + id="datasets", + set_type="dataset", + exists=False, + result_count=0, + results=[], + ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } -@router.get("/{dataset_id}", response_model=Dataset) -async def get_dataset( - dataset_id: str, +@router.post("", response_model=BeaconResultsetsResponse) +async def query_datasets( + request_body: BeaconRequestBody, service: DatasetServiceDep, -) -> Dataset: - """Retrieve a specific dataset by ID.""" +) -> dict[str, Any]: + """ + Query datasets based on filters. + + Supports different granularities: + - boolean: Returns only existence of matches + - count: Returns count of matches + - record: Returns full records + + Args: + request_body: Beacon request with query parameters and filters + service: Dataset service dependency + + Returns: + BeaconResultsetsResponse with results based on requested granularity + + Raises: + HTTPException: 501 if service not implemented + """ try: - dataset = await service.get_by_id(dataset_id) - if dataset is None: - raise HTTPException(status_code=404, detail="Dataset not found") - return dataset + granularity = request_body.meta.requested_granularity + + # Create response metadata + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity=granularity.value, + received_request_summary={ + "requested_granularity": granularity.value, + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + }, + ) + + if granularity == RequestedGranularity.BOOLEAN: + exists = await service.exists(request_body) + summary = BeaconSummaryResults(exists=exists) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } + + elif granularity == RequestedGranularity.COUNT: + count = await service.count(request_body) + summary = BeaconSummaryResults(exists=count > 0, num_total_results=count) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } + + else: # RECORD + datasets = await service.query(request_body) + result_set = ResultsetInstance( + id="datasets", + set_type="dataset", + exists=len(datasets) > 0, + result_count=len(datasets), + results=[d.model_dump() for d in datasets], + ) + summary = BeaconSummaryResults( + exists=len(datasets) > 0, + num_total_results=len(datasets), + ) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + } + except NotImplementedError: - raise HTTPException(status_code=501, detail="Service not implemented") + # Return empty but valid response for unimplemented services (beacon-verifier compliance) + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity=request_body.meta.requested_granularity.value, + received_request_summary={ + "requested_granularity": request_body.meta.requested_granularity.value, + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + }, + ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + + if request_body.meta.requested_granularity == RequestedGranularity.RECORD: + result_set = ResultsetInstance( + id="datasets", + set_type="dataset", + exists=False, + result_count=0, + results=[], + ) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + } + else: + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } diff --git a/src/beacon_api/api/dependencies.py b/src/beacon_api/api/dependencies.py index 2df194e..a00daf0 100644 --- a/src/beacon_api/api/dependencies.py +++ b/src/beacon_api/api/dependencies.py @@ -2,6 +2,10 @@ This module contains dependency injection functions for services. Implementers should modify these to return their concrete service implementations. + +By default, stub implementations are returned that raise NotImplementedError +when methods are called. This allows the API to start and respond with empty +results for beacon-verifier compliance. """ from typing import Annotated @@ -17,6 +21,15 @@ IndividualService, RunService, ) +from beacon_api.services.stubs import ( + StubAnalysisService, + StubBiosampleService, + StubCohortService, + StubDatasetService, + StubGenomicVariationService, + StubIndividualService, + StubRunService, +) def get_individual_service() -> IndividualService: @@ -26,15 +39,9 @@ def get_individual_service() -> IndividualService: Override this function to return your concrete implementation. Returns: - IndividualService instance - - Raises: - NotImplementedError: Default implementation not provided + IndividualService instance (stub by default) """ - raise NotImplementedError( - "IndividualService not implemented. " - "Please provide a concrete implementation in your application." - ) + return StubIndividualService() def get_biosample_service() -> BiosampleService: @@ -44,15 +51,9 @@ def get_biosample_service() -> BiosampleService: Override this function to return your concrete implementation. Returns: - BiosampleService instance - - Raises: - NotImplementedError: Default implementation not provided + BiosampleService instance (stub by default) """ - raise NotImplementedError( - "BiosampleService not implemented. " - "Please provide a concrete implementation in your application." - ) + return StubBiosampleService() def get_genomic_variation_service() -> GenomicVariationService: @@ -62,15 +63,9 @@ def get_genomic_variation_service() -> GenomicVariationService: Override this function to return your concrete implementation. Returns: - GenomicVariationService instance - - Raises: - NotImplementedError: Default implementation not provided + GenomicVariationService instance (stub by default) """ - raise NotImplementedError( - "GenomicVariationService not implemented. " - "Please provide a concrete implementation in your application." - ) + return StubGenomicVariationService() def get_analysis_service() -> AnalysisService: @@ -80,15 +75,9 @@ def get_analysis_service() -> AnalysisService: Override this function to return your concrete implementation. Returns: - AnalysisService instance - - Raises: - NotImplementedError: Default implementation not provided + AnalysisService instance (stub by default) """ - raise NotImplementedError( - "AnalysisService not implemented. " - "Please provide a concrete implementation in your application." - ) + return StubAnalysisService() def get_cohort_service() -> CohortService: @@ -98,15 +87,9 @@ def get_cohort_service() -> CohortService: Override this function to return your concrete implementation. Returns: - CohortService instance - - Raises: - NotImplementedError: Default implementation not provided + CohortService instance (stub by default) """ - raise NotImplementedError( - "CohortService not implemented. " - "Please provide a concrete implementation in your application." - ) + return StubCohortService() def get_dataset_service() -> DatasetService: @@ -116,15 +99,9 @@ def get_dataset_service() -> DatasetService: Override this function to return your concrete implementation. Returns: - DatasetService instance - - Raises: - NotImplementedError: Default implementation not provided + DatasetService instance (stub by default) """ - raise NotImplementedError( - "DatasetService not implemented. " - "Please provide a concrete implementation in your application." - ) + return StubDatasetService() def get_run_service() -> RunService: @@ -134,15 +111,9 @@ def get_run_service() -> RunService: Override this function to return your concrete implementation. Returns: - RunService instance - - Raises: - NotImplementedError: Default implementation not provided + RunService instance (stub by default) """ - raise NotImplementedError( - "RunService not implemented. " - "Please provide a concrete implementation in your application." - ) + return StubRunService() # Type aliases for cleaner endpoint signatures diff --git a/src/beacon_api/api/genomic_variations.py b/src/beacon_api/api/genomic_variations.py index 82aba61..f479313 100644 --- a/src/beacon_api/api/genomic_variations.py +++ b/src/beacon_api/api/genomic_variations.py @@ -2,10 +2,15 @@ from typing import Any -from fastapi import APIRouter, HTTPException, Query +from fastapi import APIRouter, HTTPException from beacon_api.api.dependencies import GenomicVariationServiceDep -from beacon_api.models.entities import GenomicVariation +from beacon_api.api.query_params import ( + FilterParam, + PaginationLimit, + PaginationSkip, + create_request_body_from_params, +) from beacon_api.models.request import ( BeaconRequestBody, RequestedGranularity, @@ -20,32 +25,102 @@ router = APIRouter(prefix="/g_variants", tags=["genomic_variations"]) -@router.get("", response_model=list[GenomicVariation]) -async def list_genomic_variations( +@router.get("", response_model=BeaconResultsetsResponse) +async def list_variations( service: GenomicVariationServiceDep, - skip: int = Query(default=0, ge=0), - limit: int = Query(default=10, ge=1, le=100), -) -> list[GenomicVariation]: - """List all genomic variations with pagination.""" - try: - return await service.list(skip=skip, limit=limit) - except NotImplementedError: - raise HTTPException(status_code=501, detail="Service not implemented") + skip: PaginationSkip = 0, + limit: PaginationLimit = 10, + filters: FilterParam = None, +) -> dict[str, Any]: + """ + List all variations with pagination and optional filters. + Args: + service: GenomicVariation service dependency + skip: Number of records to skip (default: 0) + limit: Maximum number of records to return (default: 10, max: 100) + filters: Beacon v2 filters in JSON or comma-separated format (optional) -@router.get("/{variation_id}", response_model=GenomicVariation) -async def get_genomic_variation( - variation_id: str, - service: GenomicVariationServiceDep, -) -> GenomicVariation: - """Retrieve a specific genomic variation by ID.""" + Returns: + BeaconResultsetsResponse with genomic_variation records + + Raises: + HTTPException: 400 if filters are invalid + """ try: - variation = await service.get_by_id(variation_id) - if variation is None: - raise HTTPException(status_code=404, detail="Genomic variation not found") - return variation + request_body = create_request_body_from_params( + skip=skip, + limit=limit, + granularity=RequestedGranularity.RECORD, + filters=filters, + ) + variations = await service.query(request_body) + + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + "pagination": {"skip": skip, "limit": limit}, + }, + ) + + result_set = ResultsetInstance( + id="g_variants", + set_type="genomic_variation", + exists=len(variations) > 0, + result_count=len(variations), + results=[v.model_dump() for v in variations], + ) + + summary = BeaconSummaryResults( + exists=len(variations) > 0, + num_total_results=len(variations), + ) + + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } + + except ValueError as e: + raise HTTPException(status_code=400, detail=str(e)) from None except NotImplementedError: - raise HTTPException(status_code=501, detail="Service not implemented") + # Return empty but valid response for unimplemented services + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": [], + "pagination": {"skip": skip, "limit": limit}, + }, + ) + result_set = ResultsetInstance( + id="g_variants", + set_type="genomic_variation", + exists=False, + result_count=0, + results=[], + ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } @router.post("", response_model=BeaconResultsetsResponse) @@ -53,46 +128,109 @@ async def query_genomic_variations( request_body: BeaconRequestBody, service: GenomicVariationServiceDep, ) -> dict[str, Any]: - """Query genomic variations based on filters.""" + """ + Query genomic variations based on filters. + + Supports different granularities: + - boolean: Returns only existence of matches + - count: Returns count of matches + - record: Returns full records + + Args: + request_body: Beacon request with query parameters and filters + service: Genomic variation service dependency + + Returns: + BeaconResultsetsResponse with results based on requested granularity + + Raises: + HTTPException: 501 if service not implemented + """ try: granularity = request_body.meta.requested_granularity meta = BeaconResponseMeta( beacon_id="beacon-skeleton", api_version="v2.0", returned_granularity=granularity.value, - received_request_summary={"requested_granularity": granularity.value}, + received_request_summary={ + "requested_granularity": granularity.value, + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + }, ) if granularity == RequestedGranularity.BOOLEAN: exists = await service.exists(request_body) + summary = BeaconSummaryResults(exists=exists) return { "meta": meta.model_dump(), - "response_summary": BeaconSummaryResults(exists=exists).model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, } elif granularity == RequestedGranularity.COUNT: count = await service.count(request_body) + summary = BeaconSummaryResults(exists=count > 0, num_total_results=count) return { "meta": meta.model_dump(), - "response_summary": BeaconSummaryResults( - exists=count > 0, num_total_results=count - ).model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, } - else: + else: # RECORD variations = await service.query(request_body) + result_set = ResultsetInstance( + id="g_variants", + set_type="genomic_variation", + exists=len(variations) > 0, + result_count=len(variations), + results=[v.model_dump() for v in variations], + ) + summary = BeaconSummaryResults( + exists=len(variations) > 0, num_total_results=len(variations) + ) return { "meta": meta.model_dump(), - "response_summary": BeaconSummaryResults( - exists=len(variations) > 0, num_total_results=len(variations) - ).model_dump(), - "response": [ - ResultsetInstance( - id="g_variants", - set_type="genomic_variation", - exists=len(variations) > 0, - result_count=len(variations), - results=[v.model_dump() for v in variations], - ).model_dump() - ], + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], } except NotImplementedError: - raise HTTPException(status_code=501, detail="Service not implemented") + # Return empty but valid response for unimplemented services (beacon-verifier compliance) + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity=request_body.meta.requested_granularity.value, + received_request_summary={ + "requested_granularity": request_body.meta.requested_granularity.value, + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + }, + ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + + if request_body.meta.requested_granularity == RequestedGranularity.RECORD: + result_set = ResultsetInstance( + id="g_variants", + set_type="genomic_variation", + exists=False, + result_count=0, + results=[], + ) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + } + else: + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } diff --git a/src/beacon_api/api/individuals.py b/src/beacon_api/api/individuals.py index c162818..49c932e 100644 --- a/src/beacon_api/api/individuals.py +++ b/src/beacon_api/api/individuals.py @@ -2,18 +2,20 @@ from typing import Any -from fastapi import APIRouter, HTTPException, Query +from fastapi import APIRouter, HTTPException from beacon_api.api.dependencies import IndividualServiceDep -from beacon_api.models.common import Pagination -from beacon_api.models.entities import Individual +from beacon_api.api.query_params import ( + FilterParam, + PaginationLimit, + PaginationSkip, + create_request_body_from_params, +) from beacon_api.models.request import ( BeaconRequestBody, RequestedGranularity, ) from beacon_api.models.response import ( - BeaconBooleanResponse, - BeaconCountResponse, BeaconResponseMeta, BeaconResultsetsResponse, BeaconSummaryResults, @@ -23,40 +25,113 @@ router = APIRouter(prefix="/individuals", tags=["individuals"]) -@router.get("", response_model=list[Individual]) +@router.get("", response_model=BeaconResultsetsResponse) async def list_individuals( service: IndividualServiceDep, - skip: int = Query(default=0, ge=0, description="Number of records to skip"), - limit: int = Query( - default=10, ge=1, le=100, description="Maximum number of records to return" - ), -) -> list[Individual]: + skip: PaginationSkip = 0, + limit: PaginationLimit = 10, + filters: FilterParam = None, +) -> dict[str, Any]: """ - List all individuals with pagination. + List all individuals with pagination and optional filters. + + Supports Beacon v2 filter formats: + - JSON: ?filters=[{"id":"HP:0001250"},{"id":"PATO:0000011","operator":">","value":"P70Y"}] + - Comma-separated: ?filters=HP:0001250,NCIT:C6975,PATO_0000011:>P70Y Args: service: Individual service dependency - skip: Number of records to skip - limit: Maximum number of records to return + skip: Number of records to skip (default: 0) + limit: Maximum number of records to return (default: 10, max: 100) + filters: Beacon v2 filters in JSON or comma-separated format (optional) Returns: - List of Individual objects + BeaconResultsetsResponse with individual records + + Raises: + HTTPException: 400 if filters are invalid """ try: - individuals = await service.list(skip=skip, limit=limit) - return individuals + request_body = create_request_body_from_params( + skip=skip, + limit=limit, + granularity=RequestedGranularity.RECORD, + filters=filters, + ) + individuals = await service.query(request_body) + + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + "pagination": {"skip": skip, "limit": limit}, + }, + ) + + result_set = ResultsetInstance( + id="individuals", + set_type="individual", + exists=len(individuals) > 0, + result_count=len(individuals), + results=[ind.model_dump() for ind in individuals], + ) + + summary = BeaconSummaryResults( + exists=len(individuals) > 0, + num_total_results=len(individuals), + ) + + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } + + except ValueError as e: + raise HTTPException(status_code=400, detail=str(e)) from None except NotImplementedError: - raise HTTPException( - status_code=501, - detail="Individual service not implemented. Please provide a concrete implementation.", + # Return empty but valid response for unimplemented services + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": [], + "pagination": {"skip": skip, "limit": limit}, + }, ) + result_set = ResultsetInstance( + id="individuals", + set_type="individual", + exists=False, + result_count=0, + results=[], + ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } -@router.get("/{individual_id}", response_model=Individual) +@router.get("/{individual_id}", response_model=BeaconResultsetsResponse) async def get_individual( individual_id: str, service: IndividualServiceDep, -) -> Individual: +) -> dict[str, Any]: """ Retrieve a specific individual by ID. @@ -65,22 +140,49 @@ async def get_individual( service: Individual service dependency Returns: - Individual object + BeaconResultsetsResponse containing the individual Raises: - HTTPException: 404 if individual not found, 501 if service not implemented + HTTPException: 404 if individual not found """ try: individual = await service.get_by_id(individual_id) if individual is None: raise HTTPException(status_code=404, detail="Individual not found") - return individual - except NotImplementedError: - raise HTTPException( - status_code=501, - detail="Individual service not implemented. Please provide a concrete implementation.", + + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": [], + "requested_id": individual_id, + }, + ) + + result_set = ResultsetInstance( + id="individuals", + set_type="individual", + exists=True, + result_count=1, + results=[individual.model_dump()], ) + summary = BeaconSummaryResults(exists=True, num_total_results=1) + + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } + + except NotImplementedError: + # Return 404 for unimplemented services + raise HTTPException(status_code=404, detail="Individual not found") from None + @router.post("", response_model=BeaconResultsetsResponse) async def query_individuals( @@ -102,8 +204,8 @@ async def query_individuals( Returns: BeaconResultsetsResponse with results based on requested granularity - Raises: - HTTPException: 501 if service not implemented + Note: + Returns empty response if service is not implemented (for beacon-verifier compliance) """ try: granularity = request_body.meta.requested_granularity @@ -129,6 +231,8 @@ async def query_individuals( return { "meta": meta.model_dump(), "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, } elif granularity == RequestedGranularity.COUNT: @@ -137,6 +241,8 @@ async def query_individuals( return { "meta": meta.model_dump(), "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, } else: # RECORD @@ -159,7 +265,39 @@ async def query_individuals( } except NotImplementedError: - raise HTTPException( - status_code=501, - detail="Individual service not implemented. Please provide a concrete implementation.", + # Return empty but valid response for unimplemented services (beacon-verifier compliance) + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity=request_body.meta.requested_granularity.value, + received_request_summary={ + "requested_granularity": request_body.meta.requested_granularity.value, + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + }, ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + + if request_body.meta.requested_granularity == RequestedGranularity.RECORD: + result_set = ResultsetInstance( + id="individuals", + set_type="individual", + exists=False, + result_count=0, + results=[], + ) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + } + else: + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } diff --git a/src/beacon_api/api/info.py b/src/beacon_api/api/info.py index 8f3f75c..feaed38 100644 --- a/src/beacon_api/api/info.py +++ b/src/beacon_api/api/info.py @@ -58,9 +58,9 @@ async def get_beacon_info() -> dict[str, Any]: ) meta = { - "beacon_id": settings.beacon_id, - "api_version": settings.api_version, - "returned_schemas": [], + "beaconId": settings.beacon_id, + "apiVersion": settings.api_version, + "returnedSchemas": [], } - return {"meta": meta, "response": response.model_dump()} + return {"meta": meta, "response": response.model_dump(by_alias=True)} diff --git a/src/beacon_api/api/monitor.py b/src/beacon_api/api/monitor.py index eb9df8b..f5283de 100644 --- a/src/beacon_api/api/monitor.py +++ b/src/beacon_api/api/monitor.py @@ -2,10 +2,12 @@ Provides health information about the Beacon service. """ + from fastapi import APIRouter router = APIRouter(prefix="/monitor", tags=["monitor"]) + @router.get("/health") async def health_check() -> dict[str, str]: """ diff --git a/src/beacon_api/api/query_params.py b/src/beacon_api/api/query_params.py new file mode 100644 index 0000000..12dc15b --- /dev/null +++ b/src/beacon_api/api/query_params.py @@ -0,0 +1,167 @@ +"""Helper utilities for parsing query parameters into Beacon request models.""" + +import json +from typing import Annotated + +from fastapi import Query + +from beacon_api.models.request import ( + BeaconRequestBody, + BeaconRequestParameters, + FilteringTerm, + RequestedGranularity, +) + + +def parse_filters_from_string(filters_str: str | None) -> list[FilteringTerm] | None: + """ + Parse filter string into list of FilteringTerm objects. + + Supports two formats per Beacon v2 specification: + 1. POST/JSON format: JSON string with filter objects + Example: '[{"id":"HP:0001250"},{"id":"PATO:0000011","operator":">","value":"P70Y"}]' + 2. GET format: Comma-separated filter IDs with optional operators + Example: 'NCIT:C6975,PATO_0000011:>:P70Y,HP_0032443:%cancer%' + + Args: + filters_str: Filter string in either JSON or comma-separated format + + Returns: + List of FilteringTerm objects or None if no filters provided + + Raises: + ValueError: If filter string is invalid or doesn't match FilteringTerm schema + """ + if not filters_str: + return None + + # Try JSON format first (POST requests) + if filters_str.strip().startswith("[") or filters_str.strip().startswith("{"): + try: + filters_data = json.loads(filters_str) + + # Handle single filter object + if isinstance(filters_data, dict): + return [FilteringTerm(**filters_data)] + + # Handle array of filter objects + if isinstance(filters_data, list): + return [FilteringTerm(**f) for f in filters_data] + + raise ValueError("JSON filters must be an object or array of objects") + + except json.JSONDecodeError as e: + raise ValueError(f"Invalid JSON in filters parameter: {e}") from e + except Exception as e: + raise ValueError(f"Invalid filter format: {e}") from e + + # Parse comma-separated format (GET requests) + # Per Beacon v2 spec: + # - Simple ontology: NCIT:C6975 or HP:0001250 + # - With underscores: PATO_0000011 (gets converted to PATO:0000011) + # - With operator: PATO_0000011:>P70Y (no colon between operator and value!) + # - With wildcards: HP_0032443:%cancer% + try: + filters = [] + for filter_str in filters_str.split(","): + filter_str = filter_str.strip() + if not filter_str: + continue + + # Check for operator pattern: ID:operatorVALUE or ID_operatorVALUE + # Operators can be: =, >, <, !, >=, <= + operator_match = None + for op in [">=", "<=", "=", ">", "<", "!"]: + # Try to find operator in the string + if f":{op}" in filter_str or f"_{op}" in filter_str: + # Split on operator + if f":{op}" in filter_str: + parts = filter_str.split(f":{op}", 1) + else: + parts = filter_str.split(f"_{op}", 1) + + if len(parts) == 2: + filter_id = parts[0].replace("_", ":") + value = parts[1] + # Try to convert value to number if possible + try: + if "." in value and not value.startswith("%"): + value = float(value) + elif value.isdigit(): + value = int(value) + except ValueError: + pass # Keep as string + filters.append( + FilteringTerm(id=filter_id, operator=op, value=value) + ) + operator_match = True + break + + if not operator_match: + # Simple ontology filter - just replace underscores with colons + filter_id = filter_str.replace("_", ":") + filters.append(FilteringTerm(id=filter_id)) + + return filters if filters else None + + except Exception as e: + raise ValueError( + f"Invalid filter format. Use comma-separated IDs or JSON: {e}" + ) from e + + +def create_request_body_from_params( + skip: int = 0, + limit: int = 10, + granularity: RequestedGranularity = RequestedGranularity.RECORD, + filters: str | None = None, +) -> BeaconRequestBody: + """ + Create a BeaconRequestBody from query parameters. + + Args: + skip: Number of records to skip for pagination + limit: Maximum number of records to return + granularity: Requested granularity of response + filters: JSON string of filters (single object or array) + + Returns: + BeaconRequestBody with parsed parameters + + Raises: + ValueError: If filters parameter contains invalid JSON or filter data + """ + parsed_filters = parse_filters_from_string(filters) + + return BeaconRequestBody( + meta=BeaconRequestParameters( + pagination={"skip": skip, "limit": limit}, + requested_granularity=granularity, + ), + filters=parsed_filters, + ) + + +# Type aliases for FastAPI dependency injection +PaginationSkip = Annotated[int, Query(ge=0, description="Number of records to skip")] +PaginationLimit = Annotated[ + int, + Query( + ge=1, + le=100, + description="Maximum number of records to return", + ), +] +FilterParam = Annotated[ + str | None, + Query( + description='Filters in JSON or comma-separated format. JSON: [{"id":"HP:0001250"}] or comma-separated: NCIT:C6975,PATO_0000011:>:P70Y', + ), +] +GranularityParam = Annotated[ + RequestedGranularity, + Query( + default=RequestedGranularity.BOOLEAN, + description="Requested granularity of the response (default: boolean)", + ), +] diff --git a/src/beacon_api/api/runs.py b/src/beacon_api/api/runs.py index 38ab577..405fb0d 100644 --- a/src/beacon_api/api/runs.py +++ b/src/beacon_api/api/runs.py @@ -1,36 +1,239 @@ """Beacon v2 runs endpoints.""" -from fastapi import APIRouter, HTTPException, Query +from typing import Any + +from fastapi import APIRouter, HTTPException from beacon_api.api.dependencies import RunServiceDep -from beacon_api.models.entities import Run +from beacon_api.api.query_params import ( + FilterParam, + PaginationLimit, + PaginationSkip, + create_request_body_from_params, +) +from beacon_api.models.request import BeaconRequestBody, RequestedGranularity +from beacon_api.models.response import ( + BeaconResponseMeta, + BeaconResultsetsResponse, + BeaconSummaryResults, + ResultsetInstance, +) router = APIRouter(prefix="/runs", tags=["runs"]) -@router.get("", response_model=list[Run]) +@router.get("", response_model=BeaconResultsetsResponse) async def list_runs( service: RunServiceDep, - skip: int = Query(default=0, ge=0), - limit: int = Query(default=10, ge=1, le=100), -) -> list[Run]: - """List all runs with pagination.""" + skip: PaginationSkip = 0, + limit: PaginationLimit = 10, + filters: FilterParam = None, +) -> dict[str, Any]: + """ + List all runs with pagination and optional filters. + + Args: + service: Run service dependency + skip: Number of records to skip (default: 0) + limit: Maximum number of records to return (default: 10, max: 100) + filters: Beacon v2 filters in JSON or comma-separated format (optional) + + Returns: + BeaconResultsetsResponse with run records + + Raises: + HTTPException: 400 if filters are invalid + """ try: - return await service.list(skip=skip, limit=limit) + request_body = create_request_body_from_params( + skip=skip, + limit=limit, + granularity=RequestedGranularity.RECORD, + filters=filters, + ) + runs = await service.query(request_body) + + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + "pagination": {"skip": skip, "limit": limit}, + }, + ) + + result_set = ResultsetInstance( + id="runs", + set_type="run", + exists=len(runs) > 0, + result_count=len(runs), + results=[r.model_dump() for r in runs], + ) + + summary = BeaconSummaryResults( + exists=len(runs) > 0, + num_total_results=len(runs), + ) + + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } + + except ValueError as e: + raise HTTPException(status_code=400, detail=str(e)) from None except NotImplementedError: - raise HTTPException(status_code=501, detail="Service not implemented") + # Return empty but valid response for unimplemented services + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity="record", + received_request_summary={ + "requested_granularity": "record", + "filters": [], + "pagination": {"skip": skip, "limit": limit}, + }, + ) + result_set = ResultsetInstance( + id="runs", + set_type="run", + exists=False, + result_count=0, + results=[], + ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + "info": None, + "beacon_error": None, + } -@router.get("/{run_id}", response_model=Run) -async def get_run( - run_id: str, +@router.post("", response_model=BeaconResultsetsResponse) +async def query_runs( + request_body: BeaconRequestBody, service: RunServiceDep, -) -> Run: - """Retrieve a specific run by ID.""" +) -> dict[str, Any]: + """ + Query runs based on filters. + + Supports different granularities: + - boolean: Returns only existence of matches + - count: Returns count of matches + - record: Returns full records + + Args: + request_body: Beacon request with query parameters and filters + service: Run service dependency + + Returns: + BeaconResultsetsResponse with results based on requested granularity + + Raises: + HTTPException: 501 if service not implemented + """ try: - run = await service.get_by_id(run_id) - if run is None: - raise HTTPException(status_code=404, detail="Run not found") - return run + granularity = request_body.meta.requested_granularity + + # Create response metadata + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity=granularity.value, + received_request_summary={ + "requested_granularity": granularity.value, + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + }, + ) + + if granularity == RequestedGranularity.BOOLEAN: + exists = await service.exists(request_body) + summary = BeaconSummaryResults(exists=exists) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } + + elif granularity == RequestedGranularity.COUNT: + count = await service.count(request_body) + summary = BeaconSummaryResults(exists=count > 0, num_total_results=count) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } + + else: # RECORD + runs = await service.query(request_body) + result_set = ResultsetInstance( + id="runs", + set_type="run", + exists=len(runs) > 0, + result_count=len(runs), + results=[r.model_dump() for r in runs], + ) + summary = BeaconSummaryResults( + exists=len(runs) > 0, + num_total_results=len(runs), + ) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + } + except NotImplementedError: - raise HTTPException(status_code=501, detail="Service not implemented") + # Return empty but valid response for unimplemented services (beacon-verifier compliance) + meta = BeaconResponseMeta( + beacon_id="beacon-skeleton", + api_version="v2.0", + returned_granularity=request_body.meta.requested_granularity.value, + received_request_summary={ + "requested_granularity": request_body.meta.requested_granularity.value, + "filters": ( + [f.model_dump() for f in request_body.filters] + if request_body.filters + else [] + ), + }, + ) + summary = BeaconSummaryResults(exists=False, num_total_results=0) + + if request_body.meta.requested_granularity == RequestedGranularity.RECORD: + result_set = ResultsetInstance( + id="runs", + set_type="run", + exists=False, + result_count=0, + results=[], + ) + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "response": [result_set.model_dump()], + } + else: + return { + "meta": meta.model_dump(), + "response_summary": summary.model_dump(), + "info": None, + "beacon_error": None, + } diff --git a/src/beacon_api/core/config.py b/src/beacon_api/core/config.py index 269bdef..90b05b3 100644 --- a/src/beacon_api/core/config.py +++ b/src/beacon_api/core/config.py @@ -1,20 +1,26 @@ """Application configuration using Pydantic Settings.""" from functools import lru_cache -from typing import Optional from pydantic import Field -from pydantic_settings import BaseSettings +from pydantic_settings import BaseSettings, SettingsConfigDict class Settings(BaseSettings): """Application settings loaded from environment variables.""" + model_config = SettingsConfigDict( + env_file=".env", + env_file_encoding="utf-8", + case_sensitive=False, + extra="ignore", + ) + # API Configuration api_version: str = Field(default="v2.0", description="Beacon API version") environment: str = Field( - default="development", - description="Environment: production, development, or staging", + default="dev", + description="Environment: prod, test, dev, or staging", ) # Beacon Information @@ -26,27 +32,27 @@ class Settings(BaseSettings): default="Beacon Skeleton", description="Human-readable name for this Beacon", ) - beacon_description: Optional[str] = Field( + beacon_description: str | None = Field( default="A skeleton implementation of the GA4GH Beacon v2 API", description="Description of this Beacon", ) - beacon_version: Optional[str] = Field( + beacon_version: str | None = Field( default="0.1.0", description="Version of this Beacon implementation", ) - beacon_welcome_url: Optional[str] = Field( + beacon_welcome_url: str | None = Field( default=None, description="Welcome page URL", ) - beacon_alternative_url: Optional[str] = Field( + beacon_alternative_url: str | None = Field( default=None, description="Alternative URL for this Beacon", ) - beacon_create_date_time: Optional[str] = Field( + beacon_create_date_time: str | None = Field( default=None, description="Beacon creation date and time (ISO 8601 format)", ) - beacon_update_date_time: Optional[str] = Field( + beacon_update_date_time: str | None = Field( default=None, description="Beacon last update date and time (ISO 8601 format)", ) @@ -60,23 +66,23 @@ class Settings(BaseSettings): default="Example Organization", description="Organization name", ) - organization_description: Optional[str] = Field( + organization_description: str | None = Field( default="An example organization running a Beacon", description="Organization description", ) - organization_address: Optional[str] = Field( + organization_address: str | None = Field( default=None, description="Organization address", ) - organization_welcome_url: Optional[str] = Field( + organization_welcome_url: str | None = Field( default=None, description="Organization welcome page URL", ) - organization_contact_url: Optional[str] = Field( + organization_contact_url: str | None = Field( default=None, description="Organization contact information URL", ) - organization_logo_url: Optional[str] = Field( + organization_logo_url: str | None = Field( default=None, description="Organization logo URL", ) @@ -111,16 +117,8 @@ class Settings(BaseSettings): description="Allowed headers for CORS", ) - class Config: - """Pydantic configuration.""" - - env_file = ".env" - env_file_encoding = "utf-8" - case_sensitive = False - extra = "ignore" - -@lru_cache() +@lru_cache def get_settings() -> Settings: """ Get application settings (cached). diff --git a/src/beacon_api/main.py b/src/beacon_api/main.py index 8975a56..f967eda 100644 --- a/src/beacon_api/main.py +++ b/src/beacon_api/main.py @@ -1,11 +1,11 @@ """Main FastAPI application for Beacon v2 API.""" +from collections.abc import AsyncGenerator from contextlib import asynccontextmanager -from typing import Any, AsyncGenerator +from typing import Any from fastapi import FastAPI from fastapi.middleware.cors import CORSMiddleware -from fastapi.responses import JSONResponse from beacon_api import __version__ from beacon_api.api import ( @@ -16,8 +16,8 @@ g_variations_router, individuals_router, info_router, + monitor_router, runs_router, - monitor_router ) from beacon_api.core.config import get_settings @@ -56,8 +56,8 @@ def create_app() -> FastAPI: description="A skeleton implementation of the GA4GH Beacon v2 API specification", version=__version__, lifespan=lifespan, - docs_url="/docs", - redoc_url="/redoc", + docs_url="/api/docs", + redoc_url="/api/redoc", openapi_url="/openapi.json", ) @@ -87,7 +87,7 @@ async def root() -> dict[str, Any]: return { "message": "Beacon v2 API", "version": __version__, - "docs": "/docs", + "docs": "/api/docs", "info": "/api/info", "monitor": "/api/monitor/health", } diff --git a/src/beacon_api/models/__init__.py b/src/beacon_api/models/__init__.py index b1d0c4a..b5122d1 100644 --- a/src/beacon_api/models/__init__.py +++ b/src/beacon_api/models/__init__.py @@ -5,6 +5,15 @@ ListingQuery, Pagination, ) +from beacon_api.models.entities import ( + Analysis, + Biosample, + Cohort, + Dataset, + GenomicVariation, + Individual, + Run, +) from beacon_api.models.request import ( BeaconQuery, BeaconRequestBody, @@ -14,21 +23,12 @@ RequestedGranularity, ) from beacon_api.models.response import ( - BeaconInfoResponse, - BeaconResultsetsResponse, BeaconBooleanResponse, BeaconCountResponse, + BeaconInfoResponse, + BeaconResultsetsResponse, ResultsetInstance, ) -from beacon_api.models.entities import ( - Individual, - Biosample, - GenomicVariation, - Analysis, - Cohort, - Dataset, - Run, -) __all__ = [ # Common diff --git a/src/beacon_api/models/common.py b/src/beacon_api/models/common.py index 02e435b..0ab8ab8 100644 --- a/src/beacon_api/models/common.py +++ b/src/beacon_api/models/common.py @@ -1,6 +1,6 @@ """Common Beacon v2 models and shared schemas.""" -from typing import Any, Optional +from typing import Any from pydantic import BaseModel, Field @@ -41,11 +41,11 @@ class Pagination(BaseModel): class ListingQuery(BaseModel): """Query parameters for listing endpoints.""" - pagination: Optional[Pagination] = Field( + pagination: Pagination | None = Field( default=None, description="Pagination parameters", ) - filters: Optional[list[dict[str, Any]]] = Field( + filters: list[dict[str, Any]] | None = Field( default=None, description="Filtering terms to apply", ) @@ -64,8 +64,10 @@ class SchemaReference(BaseModel): description="Version of the schema", examples=["2.0.0"], ) - schema_url: Optional[str] = Field( + schema_url: str | None = Field( default=None, description="URL to the schema definition", - examples=["https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/individuals/defaultSchema.json"], + examples=[ + "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/individuals/defaultSchema.json" + ], ) diff --git a/src/beacon_api/models/entities.py b/src/beacon_api/models/entities.py index bab7d0e..09b761d 100644 --- a/src/beacon_api/models/entities.py +++ b/src/beacon_api/models/entities.py @@ -1,6 +1,6 @@ """Beacon v2 entity models (individuals, biosamples, variations, etc.).""" -from typing import Any, Optional +from typing import Any from pydantic import BaseModel, Field @@ -9,36 +9,36 @@ class Individual(BaseModel): """Individual/subject entity model.""" id: str = Field(..., description="Individual identifier") - sex: Optional[str] = Field( + sex: str | None = Field( default=None, description="Sex of the individual", examples=["MALE", "FEMALE", "OTHER_SEX", "UNKNOWN_SEX"], ) - ethnicity: Optional[dict[str, Any]] = Field( + ethnicity: dict[str, Any] | None = Field( default=None, description="Ethnic background ontology term", ) - geographic_origin: Optional[dict[str, Any]] = Field( + geographic_origin: dict[str, Any] | None = Field( default=None, description="Geographic origin ontology term", ) - diseases: Optional[list[dict[str, Any]]] = Field( + diseases: list[dict[str, Any]] | None = Field( default=None, description="List of diseases associated with the individual", ) - phenotypic_features: Optional[list[dict[str, Any]]] = Field( + phenotypic_features: list[dict[str, Any]] | None = Field( default=None, description="List of phenotypic features", ) - interventions_or_procedures: Optional[list[dict[str, Any]]] = Field( + interventions_or_procedures: list[dict[str, Any]] | None = Field( default=None, description="List of interventions or procedures", ) - measures: Optional[list[dict[str, Any]]] = Field( + measures: list[dict[str, Any]] | None = Field( default=None, description="List of measurements", ) - info: Optional[dict[str, Any]] = Field( + info: dict[str, Any] | None = Field( default=None, description="Additional information", ) @@ -48,63 +48,63 @@ class Biosample(BaseModel): """Biosample entity model.""" id: str = Field(..., description="Biosample identifier") - individual_id: Optional[str] = Field( + individual_id: str | None = Field( default=None, description="Reference to the individual this biosample was derived from", ) - biosample_status: Optional[dict[str, Any]] = Field( + biosample_status: dict[str, Any] | None = Field( default=None, description="Status of the biosample", ) - sample_origin_type: Optional[dict[str, Any]] = Field( + sample_origin_type: dict[str, Any] | None = Field( default=None, description="Type of sample origin", ) - sample_origin_detail: Optional[dict[str, Any]] = Field( + sample_origin_detail: dict[str, Any] | None = Field( default=None, description="Detailed information about sample origin", ) - collection_date: Optional[str] = Field( + collection_date: str | None = Field( default=None, description="Date when the sample was collected", ) - collection_moment: Optional[str] = Field( + collection_moment: str | None = Field( default=None, description="Moment in time when sample was collected", ) - obtained_from_id: Optional[str] = Field( + obtained_from_id: str | None = Field( default=None, description="ID of the biosample this sample was obtained from", ) - phenotypic_features: Optional[list[dict[str, Any]]] = Field( + phenotypic_features: list[dict[str, Any]] | None = Field( default=None, description="List of phenotypic features", ) - measurements: Optional[list[dict[str, Any]]] = Field( + measurements: list[dict[str, Any]] | None = Field( default=None, description="List of measurements", ) - pathological_stage: Optional[dict[str, Any]] = Field( + pathological_stage: dict[str, Any] | None = Field( default=None, description="Pathological stage of the sample", ) - tumor_progression: Optional[dict[str, Any]] = Field( + tumor_progression: dict[str, Any] | None = Field( default=None, description="Tumor progression status", ) - tumor_grade: Optional[dict[str, Any]] = Field( + tumor_grade: dict[str, Any] | None = Field( default=None, description="Tumor grade", ) - diagnostic_markers: Optional[list[dict[str, Any]]] = Field( + diagnostic_markers: list[dict[str, Any]] | None = Field( default=None, description="List of diagnostic markers", ) - procedure: Optional[dict[str, Any]] = Field( + procedure: dict[str, Any] | None = Field( default=None, description="Procedure used to collect the sample", ) - info: Optional[dict[str, Any]] = Field( + info: dict[str, Any] | None = Field( default=None, description="Additional information", ) @@ -114,48 +114,48 @@ class GenomicVariation(BaseModel): """Genomic variation entity model.""" id: str = Field(..., description="Variation identifier") - variation_type: Optional[str] = Field( + variation_type: str | None = Field( default=None, description="Type of variation", examples=["SNP", "DEL", "INS", "DUP", "INV", "CNV"], ) - reference_genome: Optional[str] = Field( + reference_genome: str | None = Field( default=None, description="Reference genome assembly", examples=["GRCh38", "GRCh37"], ) - chromosome: Optional[str] = Field( + chromosome: str | None = Field( default=None, description="Chromosome name", examples=["1", "22", "X", "Y", "MT"], ) - start: Optional[int] = Field( + start: int | None = Field( default=None, description="Start position (0-based)", ge=0, ) - end: Optional[int] = Field( + end: int | None = Field( default=None, description="End position (0-based)", ge=0, ) - reference_bases: Optional[str] = Field( + reference_bases: str | None = Field( default=None, description="Reference bases", ) - alternate_bases: Optional[str] = Field( + alternate_bases: str | None = Field( default=None, description="Alternate bases", ) - variant_internal_id: Optional[str] = Field( + variant_internal_id: str | None = Field( default=None, description="Internal variant identifier", ) - identifiers: Optional[dict[str, Any]] = Field( + identifiers: dict[str, Any] | None = Field( default=None, description="External identifiers for this variation", ) - info: Optional[dict[str, Any]] = Field( + info: dict[str, Any] | None = Field( default=None, description="Additional information", ) @@ -165,35 +165,35 @@ class Analysis(BaseModel): """Analysis entity model.""" id: str = Field(..., description="Analysis identifier") - analysis_type: Optional[dict[str, Any]] = Field( + analysis_type: dict[str, Any] | None = Field( default=None, description="Type of analysis performed", ) - pipeline_name: Optional[str] = Field( + pipeline_name: str | None = Field( default=None, description="Name of the analysis pipeline", ) - pipeline_ref: Optional[str] = Field( + pipeline_ref: str | None = Field( default=None, description="Reference to the pipeline (e.g., URL, DOI)", ) - analysis_date: Optional[str] = Field( + analysis_date: str | None = Field( default=None, description="Date when the analysis was performed", ) - biosample_id: Optional[str] = Field( + biosample_id: str | None = Field( default=None, description="Reference to the biosample analyzed", ) - individual_id: Optional[str] = Field( + individual_id: str | None = Field( default=None, description="Reference to the individual analyzed", ) - run_id: Optional[str] = Field( + run_id: str | None = Field( default=None, description="Reference to the sequencing run", ) - info: Optional[dict[str, Any]] = Field( + info: dict[str, Any] | None = Field( default=None, description="Additional information", ) @@ -204,33 +204,33 @@ class Cohort(BaseModel): id: str = Field(..., description="Cohort identifier") name: str = Field(..., description="Cohort name") - cohort_type: Optional[str] = Field( + cohort_type: str | None = Field( default=None, description="Type of cohort", examples=["study-defined", "beacon-defined"], ) - cohort_size: Optional[int] = Field( + cohort_size: int | None = Field( default=None, description="Number of individuals in the cohort", ge=0, ) - cohort_data_types: Optional[list[dict[str, Any]]] = Field( + cohort_data_types: list[dict[str, Any]] | None = Field( default=None, description="Types of data available for this cohort", ) - collection_events: Optional[list[dict[str, Any]]] = Field( + collection_events: list[dict[str, Any]] | None = Field( default=None, description="Collection events for this cohort", ) - inclusion_criteria: Optional[dict[str, Any]] = Field( + inclusion_criteria: dict[str, Any] | None = Field( default=None, description="Inclusion criteria for the cohort", ) - exclusion_criteria: Optional[dict[str, Any]] = Field( + exclusion_criteria: dict[str, Any] | None = Field( default=None, description="Exclusion criteria for the cohort", ) - info: Optional[dict[str, Any]] = Field( + info: dict[str, Any] | None = Field( default=None, description="Additional information", ) @@ -241,36 +241,36 @@ class Dataset(BaseModel): id: str = Field(..., description="Dataset identifier") name: str = Field(..., description="Dataset name") - description: Optional[str] = Field( + description: str | None = Field( default=None, description="Dataset description", ) - assembly_id: Optional[str] = Field( + assembly_id: str | None = Field( default=None, description="Reference genome assembly", examples=["GRCh38", "GRCh37"], ) - create_date_time: Optional[str] = Field( + create_date_time: str | None = Field( default=None, description="Dataset creation date and time", ) - update_date_time: Optional[str] = Field( + update_date_time: str | None = Field( default=None, description="Dataset last update date and time", ) - version: Optional[str] = Field( + version: str | None = Field( default=None, description="Dataset version", ) - external_url: Optional[str] = Field( + external_url: str | None = Field( default=None, description="External URL for the dataset", ) - data_use_conditions: Optional[dict[str, Any]] = Field( + data_use_conditions: dict[str, Any] | None = Field( default=None, description="Data use conditions and restrictions", ) - info: Optional[dict[str, Any]] = Field( + info: dict[str, Any] | None = Field( default=None, description="Additional information", ) @@ -280,47 +280,47 @@ class Run(BaseModel): """Sequencing run entity model.""" id: str = Field(..., description="Run identifier") - biosample_id: Optional[str] = Field( + biosample_id: str | None = Field( default=None, description="Reference to the biosample sequenced", ) - individual_id: Optional[str] = Field( + individual_id: str | None = Field( default=None, description="Reference to the individual sequenced", ) - run_date: Optional[str] = Field( + run_date: str | None = Field( default=None, description="Date when the run was performed", ) - library_source: Optional[str] = Field( + library_source: str | None = Field( default=None, description="Source of the library", examples=["GENOMIC", "TRANSCRIPTOMIC", "METAGENOMIC"], ) - library_selection: Optional[str] = Field( + library_selection: str | None = Field( default=None, description="Library selection method", ) - library_strategy: Optional[str] = Field( + library_strategy: str | None = Field( default=None, description="Library strategy", examples=["WGS", "WXS", "RNA-Seq", "ChIP-Seq"], ) - library_layout: Optional[str] = Field( + library_layout: str | None = Field( default=None, description="Library layout", examples=["SINGLE", "PAIRED"], ) - platform: Optional[str] = Field( + platform: str | None = Field( default=None, description="Sequencing platform", examples=["ILLUMINA", "PACBIO", "OXFORD_NANOPORE"], ) - platform_model: Optional[str] = Field( + platform_model: str | None = Field( default=None, description="Specific platform model", ) - info: Optional[dict[str, Any]] = Field( + info: dict[str, Any] | None = Field( default=None, description="Additional information", ) diff --git a/src/beacon_api/models/request.py b/src/beacon_api/models/request.py index 44e0a59..d998535 100644 --- a/src/beacon_api/models/request.py +++ b/src/beacon_api/models/request.py @@ -1,7 +1,6 @@ """Beacon v2 request models.""" from enum import Enum -from typing import Any, Optional from pydantic import BaseModel, Field @@ -15,55 +14,59 @@ class RequestedGranularity(str, Enum): class OntologyFilter(BaseModel): - """Ontology-based filter.""" + """Ontology-based filter for Beacon v2. + + Used for bio-ontology term queries identified by CURIE format. + """ id: str = Field( ..., - description="Ontology term ID", - examples=["HP:0001250", "NCIT:C3058"], - ) - scope: Optional[str] = Field( - default=None, - description="Scope of the ontology filter", - examples=["individuals", "biosamples"], + description="Ontology term ID in CURIE format", + examples=["HP:0001250", "NCIT:C3058", "HP:0100526"], ) - include_descendant_terms: bool = Field( - default=False, - description="Include descendant terms in the query", + includeDescendantTerms: bool = Field( + default=True, + description="Include descendant terms in the query (default: true)", ) - similarity: Optional[str] = Field( + similarity: str | None = Field( default=None, description="Similarity matching method", - examples=["exact", "high", "medium", "low"], + examples=["high", "medium", "low"], ) class FilteringTerm(BaseModel): - """Generic filtering term for Beacon queries.""" + """Filtering term for Beacon v2 queries. - type: str = Field( + Supports three filter types: + 1. Ontology filters: Only 'id' required, optionally with includeDescendantTerms/similarity + 2. Alphanumeric/Numeric filters: Requires 'id', 'operator', and 'value' + 3. Custom filters: Locally-defined with unique identifiers + """ + + id: str = Field( ..., - description="Type of the filter", - examples=["ontology", "alphanumeric", "numeric"], + description="Filter identifier (CURIE for ontology, field ID for alphanumeric)", + examples=["HP:0001250", "PATO:0000011", "NCIT:C6975"], ) - id: Optional[str] = Field( + operator: str | None = Field( default=None, - description="Filter ID (for ontology filters)", - examples=["HP:0001250"], + description="Comparison operator for alphanumeric/numeric filters", + examples=["=", ">", "<", "!", ">=", "<="], ) - operator: Optional[str] = Field( + value: str | int | float | None = Field( default=None, - description="Comparison operator", - examples=["=", ">", "<", ">=", "<="], + description="Filter value (ISO8601 for dates, wildcards % supported)", + examples=["P70Y", "cancer", 100, "%breast%"], ) - value: Optional[Any] = Field( + includeDescendantTerms: bool | None = Field( default=None, - description="Filter value", + description="For ontology filters: include descendant terms (default: true)", ) - scope: Optional[str] = Field( + similarity: str | None = Field( default=None, - description="Scope of the filter", - examples=["individuals", "biosamples"], + description="For ontology filters: similarity level", + examples=["high", "medium", "low"], ) @@ -74,12 +77,12 @@ class BeaconRequestParameters(BaseModel): default=RequestedGranularity.BOOLEAN, description="Requested granularity of the response", ) - include_resultset_responses: Optional[str] = Field( + include_resultset_responses: str | None = Field( default="HIT", description="Defines the level of detail in the response", examples=["HIT", "ALL", "MISS", "NONE"], ) - pagination: Optional[dict[str, int]] = Field( + pagination: dict[str, int] | None = Field( default=None, description="Pagination parameters", examples=[{"skip": 0, "limit": 10}], @@ -89,47 +92,47 @@ class BeaconRequestParameters(BaseModel): class BeaconQuery(BaseModel): """Beacon query parameters for genomic variations.""" - assembly_id: Optional[str] = Field( + assembly_id: str | None = Field( default=None, description="Assembly identifier (GRC notation)", examples=["GRCh38", "GRCh37"], ) - reference_name: Optional[str] = Field( + reference_name: str | None = Field( default=None, description="Reference sequence name", examples=["1", "22", "X", "Y", "MT", "chr1"], ) - reference_bases: Optional[str] = Field( + reference_bases: str | None = Field( default=None, description="Reference bases", examples=["A", "T", "C", "G"], ) - alternate_bases: Optional[str] = Field( + alternate_bases: str | None = Field( default=None, description="Alternate bases", examples=["A", "T", "C", "G"], ) - start: Optional[list[int]] = Field( + start: list[int] | None = Field( default=None, description="Start position(s) in 0-based coordinates", examples=[[100000, 200000]], ) - end: Optional[list[int]] = Field( + end: list[int] | None = Field( default=None, description="End position(s) in 0-based coordinates", examples=[[100100, 200100]], ) - variant_type: Optional[str] = Field( + variant_type: str | None = Field( default=None, description="Type of variant", examples=["SNP", "DEL", "INS", "DUP", "INV", "CNV"], ) - variant_min_length: Optional[int] = Field( + variant_min_length: int | None = Field( default=None, description="Minimum length of the variant", ge=0, ) - variant_max_length: Optional[int] = Field( + variant_max_length: int | None = Field( default=None, description="Maximum length of the variant", ge=0, @@ -143,11 +146,11 @@ class BeaconRequestBody(BaseModel): default_factory=BeaconRequestParameters, description="Request metadata and parameters", ) - query: Optional[BeaconQuery] = Field( + query: BeaconQuery | None = Field( default=None, description="Query parameters", ) - filters: Optional[list[FilteringTerm]] = Field( + filters: list[FilteringTerm] | None = Field( default=None, description="Filtering terms to apply", ) diff --git a/src/beacon_api/models/response.py b/src/beacon_api/models/response.py index c040195..1af4839 100644 --- a/src/beacon_api/models/response.py +++ b/src/beacon_api/models/response.py @@ -1,6 +1,6 @@ """Beacon v2 response models.""" -from typing import Any, Optional +from typing import Any from pydantic import BaseModel, Field @@ -12,59 +12,70 @@ class BeaconOrganization(BaseModel): id: str = Field(..., description="Organization identifier") name: str = Field(..., description="Organization name") - description: Optional[str] = Field( + description: str | None = Field( default=None, description="Organization description", ) - address: Optional[str] = Field(default=None, description="Organization address") - welcome_url: Optional[str] = Field( + address: str | None = Field(default=None, description="Organization address") + welcome_url: str | None = Field( default=None, description="Welcome page URL", ) - contact_url: Optional[str] = Field( + contact_url: str | None = Field( default=None, description="Contact information URL", ) - logo_url: Optional[str] = Field(default=None, description="Organization logo URL") + logo_url: str | None = Field(default=None, description="Organization logo URL") class BeaconInformationalResponse(BaseModel): """Beacon informational metadata.""" + model_config = {"populate_by_name": True} + id: str = Field(..., description="Beacon identifier") name: str = Field(..., description="Beacon name") - api_version: str = Field(..., description="Beacon API version", examples=["v2.0"]) + api_version: str = Field( + ..., + alias="apiVersion", + description="Beacon API version", + examples=["v2.0"], + ) environment: str = Field( ..., description="Beacon environment", - examples=["production", "development", "staging"], + examples=["prod", "test", "dev", "staging"], ) organization: BeaconOrganization = Field( ..., description="Organization running this Beacon", ) - description: Optional[str] = Field( + description: str | None = Field( default=None, description="Beacon description", ) - version: Optional[str] = Field( + version: str | None = Field( default=None, description="Beacon implementation version", ) - welcome_url: Optional[str] = Field( + welcome_url: str | None = Field( default=None, + alias="welcomeUrl", description="Welcome page URL", ) - alternative_url: Optional[str] = Field( + alternative_url: str | None = Field( default=None, + alias="alternativeUrl", description="Alternative URL for this Beacon", ) - create_date_time: Optional[str] = Field( + create_date_time: str | None = Field( default=None, + alias="createDateTime", description="Beacon creation date and time", ) - update_date_time: Optional[str] = Field( + update_date_time: str | None = Field( default=None, + alias="updateDateTime", description="Beacon last update date and time", ) @@ -89,7 +100,7 @@ class BeaconSummaryResults(BaseModel): ..., description="Whether any results were found", ) - num_total_results: Optional[int] = Field( + num_total_results: int | None = Field( default=None, description="Total number of results", ) @@ -105,19 +116,19 @@ class ResultsetInstance(BaseModel): examples=["dataset", "individual", "biosample"], ) exists: bool = Field(..., description="Whether results exist in this set") - result_count: Optional[int] = Field( + result_count: int | None = Field( default=None, description="Number of results in this set", ) - results: Optional[list[dict[str, Any]]] = Field( + results: list[dict[str, Any]] | None = Field( default=None, description="Actual result records", ) - info: Optional[dict[str, Any]] = Field( + info: dict[str, Any] | None = Field( default=None, description="Additional information about the result set", ) - results_handover: Optional[list[dict[str, Any]]] = Field( + results_handover: list[dict[str, Any]] | None = Field( default=None, description="Handover information for accessing full results", ) @@ -137,7 +148,7 @@ class BeaconResponseMeta(BaseModel): ..., description="Summary of the received request", ) - returned_schemas: Optional[list[SchemaReference]] = Field( + returned_schemas: list[SchemaReference] | None = Field( default=None, description="Schemas used in the response", ) @@ -151,11 +162,11 @@ class BeaconBooleanResponse(BaseModel): ..., description="Summary of query results", ) - info: Optional[dict[str, Any]] = Field( + info: dict[str, Any] | None = Field( default=None, description="Additional information", ) - beacon_error: Optional[BeaconError] = Field( + beacon_error: BeaconError | None = Field( default=None, description="Error information if query failed", ) @@ -169,11 +180,11 @@ class BeaconCountResponse(BaseModel): ..., description="Summary of query results", ) - info: Optional[dict[str, Any]] = Field( + info: dict[str, Any] | None = Field( default=None, description="Additional information", ) - beacon_error: Optional[BeaconError] = Field( + beacon_error: BeaconError | None = Field( default=None, description="Error information if query failed", ) @@ -187,15 +198,15 @@ class BeaconResultsetsResponse(BaseModel): ..., description="Summary of query results", ) - response: Optional[list[ResultsetInstance]] = Field( + response: list[ResultsetInstance] | None = Field( default=None, description="Result sets", ) - info: Optional[dict[str, Any]] = Field( + info: dict[str, Any] | None = Field( default=None, description="Additional information", ) - beacon_error: Optional[BeaconError] = Field( + beacon_error: BeaconError | None = Field( default=None, description="Error information if query failed", ) diff --git a/src/beacon_api/services/__init__.py b/src/beacon_api/services/__init__.py index a66d2ae..a007078 100644 --- a/src/beacon_api/services/__init__.py +++ b/src/beacon_api/services/__init__.py @@ -1,13 +1,13 @@ """Service layer interfaces for Beacon v2 implementation.""" from beacon_api.services.base import ( + AnalysisService, BaseBeaconService, - IndividualService, BiosampleService, - GenomicVariationService, - AnalysisService, CohortService, DatasetService, + GenomicVariationService, + IndividualService, RunService, ) diff --git a/src/beacon_api/services/base.py b/src/beacon_api/services/base.py index 9eefcca..2be8560 100644 --- a/src/beacon_api/services/base.py +++ b/src/beacon_api/services/base.py @@ -8,7 +8,6 @@ from __future__ import annotations from abc import ABC, abstractmethod -from typing import Any, Optional from beacon_api.models.entities import ( Analysis, @@ -19,31 +18,12 @@ Individual, Run, ) -from beacon_api.models.request import BeaconRequestBody, FilteringTerm +from beacon_api.models.request import BeaconRequestBody class BaseBeaconService(ABC): """Base interface for all Beacon services.""" - @abstractmethod - async def query( - self, - request_body: BeaconRequestBody, - ) -> dict[str, Any]: - """ - Execute a Beacon query. - - Args: - request_body: Complete Beacon request including query and filters - - Returns: - Dictionary containing query results - - Raises: - NotImplementedError: Must be implemented by subclass - """ - raise NotImplementedError - @abstractmethod async def count( self, @@ -61,7 +41,7 @@ async def count( Raises: NotImplementedError: Must be implemented by subclass """ - raise NotImplementedError + pass @abstractmethod async def exists( @@ -80,14 +60,14 @@ async def exists( Raises: NotImplementedError: Must be implemented by subclass """ - raise NotImplementedError + pass -class IndividualService(ABC): +class IndividualService(BaseBeaconService): """Service interface for Individual entity operations.""" @abstractmethod - async def get_by_id(self, individual_id: str) -> Optional[Individual]: + async def get_by_id(self, individual_id: str) -> Individual | None: """ Retrieve an individual by ID. @@ -102,29 +82,6 @@ async def get_by_id(self, individual_id: str) -> Optional[Individual]: """ raise NotImplementedError - @abstractmethod - async def list( - self, - skip: int = 0, - limit: int = 10, - filters: Optional[list[FilteringTerm]] = None, - ) -> list[Individual]: - """ - List individuals with optional filtering and pagination. - - Args: - skip: Number of records to skip - limit: Maximum number of records to return - filters: Optional filtering terms - - Returns: - List of Individual objects - - Raises: - NotImplementedError: Must be implemented by subclass - """ - raise NotImplementedError - @abstractmethod async def query( self, @@ -145,11 +102,11 @@ async def query( raise NotImplementedError -class BiosampleService(ABC): +class BiosampleService(BaseBeaconService): """Service interface for Biosample entity operations.""" @abstractmethod - async def get_by_id(self, biosample_id: str) -> Optional[Biosample]: + async def get_by_id(self, biosample_id: str) -> Biosample | None: """ Retrieve a biosample by ID. @@ -164,29 +121,6 @@ async def get_by_id(self, biosample_id: str) -> Optional[Biosample]: """ raise NotImplementedError - @abstractmethod - async def list( - self, - skip: int = 0, - limit: int = 10, - filters: Optional[list[FilteringTerm]] = None, - ) -> list[Biosample]: - """ - List biosamples with optional filtering and pagination. - - Args: - skip: Number of records to skip - limit: Maximum number of records to return - filters: Optional filtering terms - - Returns: - List of Biosample objects - - Raises: - NotImplementedError: Must be implemented by subclass - """ - raise NotImplementedError - @abstractmethod async def query( self, @@ -207,11 +141,11 @@ async def query( raise NotImplementedError -class GenomicVariationService(ABC): +class GenomicVariationService(BaseBeaconService): """Service interface for GenomicVariation entity operations.""" @abstractmethod - async def get_by_id(self, variation_id: str) -> Optional[GenomicVariation]: + async def get_by_id(self, variation_id: str) -> GenomicVariation | None: """ Retrieve a genomic variation by ID. @@ -226,29 +160,6 @@ async def get_by_id(self, variation_id: str) -> Optional[GenomicVariation]: """ raise NotImplementedError - @abstractmethod - async def list( - self, - skip: int = 0, - limit: int = 10, - filters: Optional[list[FilteringTerm]] = None, - ) -> list[GenomicVariation]: - """ - List genomic variations with optional filtering and pagination. - - Args: - skip: Number of records to skip - limit: Maximum number of records to return - filters: Optional filtering terms - - Returns: - List of GenomicVariation objects - - Raises: - NotImplementedError: Must be implemented by subclass - """ - raise NotImplementedError - @abstractmethod async def query( self, @@ -269,11 +180,11 @@ async def query( raise NotImplementedError -class AnalysisService(ABC): +class AnalysisService(BaseBeaconService): """Service interface for Analysis entity operations.""" @abstractmethod - async def get_by_id(self, analysis_id: str) -> Optional[Analysis]: + async def get_by_id(self, analysis_id: str) -> Analysis | None: """ Retrieve an analysis by ID. @@ -289,22 +200,18 @@ async def get_by_id(self, analysis_id: str) -> Optional[Analysis]: raise NotImplementedError @abstractmethod - async def list( + async def query( self, - skip: int = 0, - limit: int = 10, - filters: Optional[list[FilteringTerm]] = None, + request_body: BeaconRequestBody, ) -> list[Analysis]: """ - List analyses with optional filtering and pagination. + Query analyses based on Beacon request. Args: - skip: Number of records to skip - limit: Maximum number of records to return - filters: Optional filtering terms + request_body: Complete Beacon request including query and filters Returns: - List of Analysis objects + List of matching Analysis objects Raises: NotImplementedError: Must be implemented by subclass @@ -312,11 +219,11 @@ async def list( raise NotImplementedError -class CohortService(ABC): +class CohortService(BaseBeaconService): """Service interface for Cohort entity operations.""" @abstractmethod - async def get_by_id(self, cohort_id: str) -> Optional[Cohort]: + async def get_by_id(self, cohort_id: str) -> Cohort | None: """ Retrieve a cohort by ID. @@ -332,22 +239,18 @@ async def get_by_id(self, cohort_id: str) -> Optional[Cohort]: raise NotImplementedError @abstractmethod - async def list( + async def query( self, - skip: int = 0, - limit: int = 10, - filters: Optional[list[FilteringTerm]] = None, + request_body: BeaconRequestBody, ) -> list[Cohort]: """ - List cohorts with optional filtering and pagination. + Query cohorts based on Beacon request. Args: - skip: Number of records to skip - limit: Maximum number of records to return - filters: Optional filtering terms + request_body: Complete Beacon request including query and filters Returns: - List of Cohort objects + List of matching Cohort objects Raises: NotImplementedError: Must be implemented by subclass @@ -355,11 +258,11 @@ async def list( raise NotImplementedError -class DatasetService(ABC): +class DatasetService(BaseBeaconService): """Service interface for Dataset entity operations.""" @abstractmethod - async def get_by_id(self, dataset_id: str) -> Optional[Dataset]: + async def get_by_id(self, dataset_id: str) -> Dataset | None: """ Retrieve a dataset by ID. @@ -375,20 +278,18 @@ async def get_by_id(self, dataset_id: str) -> Optional[Dataset]: raise NotImplementedError @abstractmethod - async def list( + async def query( self, - skip: int = 0, - limit: int = 10, + request_body: BeaconRequestBody, ) -> list[Dataset]: """ - List datasets with optional pagination. + Query datasets based on Beacon request. Args: - skip: Number of records to skip - limit: Maximum number of records to return + request_body: Complete Beacon request including query and filters Returns: - List of Dataset objects + List of matching Dataset objects Raises: NotImplementedError: Must be implemented by subclass @@ -396,11 +297,11 @@ async def list( raise NotImplementedError -class RunService(ABC): +class RunService(BaseBeaconService): """Service interface for Run entity operations.""" @abstractmethod - async def get_by_id(self, run_id: str) -> Optional[Run]: + async def get_by_id(self, run_id: str) -> Run | None: """ Retrieve a run by ID. @@ -416,22 +317,18 @@ async def get_by_id(self, run_id: str) -> Optional[Run]: raise NotImplementedError @abstractmethod - async def list( + async def query( self, - skip: int = 0, - limit: int = 10, - filters: Optional[list[FilteringTerm]] = None, + request_body: BeaconRequestBody, ) -> list[Run]: """ - List runs with optional filtering and pagination. + Query runs based on Beacon request. Args: - skip: Number of records to skip - limit: Maximum number of records to return - filters: Optional filtering terms + request_body: Complete Beacon request including query and filters Returns: - List of Run objects + List of matching Run objects Raises: NotImplementedError: Must be implemented by subclass diff --git a/src/beacon_api/services/stubs.py b/src/beacon_api/services/stubs.py new file mode 100644 index 0000000..dc7f8b0 --- /dev/null +++ b/src/beacon_api/services/stubs.py @@ -0,0 +1,169 @@ +"""Stub service implementations for Beacon API. + +These implementations allow the API to start and respond to requests +without a backend implementation, which is useful for beacon-verifier +compliance and development/testing. + +All methods raise NotImplementedError when called, which the endpoint +handlers catch and convert to appropriate empty responses. +""" + +from beacon_api.models.entities import ( + Analysis, + Biosample, + Cohort, + Dataset, + GenomicVariation, + Individual, + Run, +) +from beacon_api.models.request import BeaconRequestBody +from beacon_api.services.base import ( + AnalysisService, + BiosampleService, + CohortService, + DatasetService, + GenomicVariationService, + IndividualService, + RunService, +) + + +class StubIndividualService(IndividualService): + """Stub implementation of IndividualService.""" + + async def get_by_id(self, individual_id: str) -> Individual | None: + """Get individual by ID - not implemented.""" + raise NotImplementedError("IndividualService not implemented") + + async def query(self, request_body: BeaconRequestBody) -> list[Individual]: + """Query individuals - not implemented.""" + raise NotImplementedError("IndividualService not implemented") + + async def count(self, request_body: BeaconRequestBody) -> int: + """Count individuals - returns 0.""" + return 0 + + async def exists(self, request_body: BeaconRequestBody) -> bool: + """Check if individuals exist - returns False.""" + return False + + +class StubBiosampleService(BiosampleService): + """Stub implementation of BiosampleService.""" + + async def get_by_id(self, biosample_id: str) -> Biosample | None: + """Get biosample by ID - not implemented.""" + raise NotImplementedError("BiosampleService not implemented") + + async def query(self, request_body: BeaconRequestBody) -> list[Biosample]: + """Query biosamples - not implemented.""" + raise NotImplementedError("BiosampleService not implemented") + + async def count(self, request_body: BeaconRequestBody) -> int: + """Count biosamples - returns 0.""" + return 0 + + async def exists(self, request_body: BeaconRequestBody) -> bool: + """Check if biosamples exist - returns False.""" + return False + + +class StubGenomicVariationService(GenomicVariationService): + """Stub implementation of GenomicVariationService.""" + + async def get_by_id(self, variation_id: str) -> GenomicVariation | None: + """Get genomic variation by ID - not implemented.""" + raise NotImplementedError("GenomicVariationService not implemented") + + async def query(self, request_body: BeaconRequestBody) -> list[GenomicVariation]: + """Query genomic variations - not implemented.""" + raise NotImplementedError("GenomicVariationService not implemented") + + async def count(self, request_body: BeaconRequestBody) -> int: + """Count genomic variations - returns 0.""" + return 0 + + async def exists(self, request_body: BeaconRequestBody) -> bool: + """Check if genomic variations exist - returns False.""" + return False + + +class StubAnalysisService(AnalysisService): + """Stub implementation of AnalysisService.""" + + async def get_by_id(self, analysis_id: str) -> Analysis | None: + """Get analysis by ID - not implemented.""" + raise NotImplementedError("AnalysisService not implemented") + + async def query(self, request_body: BeaconRequestBody) -> list[Analysis]: + """Query analyses - not implemented.""" + raise NotImplementedError("AnalysisService not implemented") + + async def count(self, request_body: BeaconRequestBody) -> int: + """Count analyses - returns 0.""" + return 0 + + async def exists(self, request_body: BeaconRequestBody) -> bool: + """Check if analyses exist - returns False.""" + return False + + +class StubCohortService(CohortService): + """Stub implementation of CohortService.""" + + async def get_by_id(self, cohort_id: str) -> Cohort | None: + """Get cohort by ID - not implemented.""" + raise NotImplementedError("CohortService not implemented") + + async def query(self, request_body: BeaconRequestBody) -> list[Cohort]: + """Query cohorts - not implemented.""" + raise NotImplementedError("CohortService not implemented") + + async def count(self, request_body: BeaconRequestBody) -> int: + """Count cohorts - returns 0.""" + return 0 + + async def exists(self, request_body: BeaconRequestBody) -> bool: + """Check if cohorts exist - returns False.""" + return False + + +class StubDatasetService(DatasetService): + """Stub implementation of DatasetService.""" + + async def get_by_id(self, dataset_id: str) -> Dataset | None: + """Get dataset by ID - not implemented.""" + raise NotImplementedError("DatasetService not implemented") + + async def query(self, request_body: BeaconRequestBody) -> list[Dataset]: + """Query datasets - not implemented.""" + raise NotImplementedError("DatasetService not implemented") + + async def count(self, request_body: BeaconRequestBody) -> int: + """Count datasets - returns 0.""" + return 0 + + async def exists(self, request_body: BeaconRequestBody) -> bool: + """Check if datasets exist - returns False.""" + return False + + +class StubRunService(RunService): + """Stub implementation of RunService.""" + + async def get_by_id(self, run_id: str) -> Run | None: + """Get run by ID - not implemented.""" + raise NotImplementedError("RunService not implemented") + + async def query(self, request_body: BeaconRequestBody) -> list[Run]: + """Query runs - not implemented.""" + raise NotImplementedError("RunService not implemented") + + async def count(self, request_body: BeaconRequestBody) -> int: + """Count runs - returns 0.""" + return 0 + + async def exists(self, request_body: BeaconRequestBody) -> bool: + """Check if runs exist - returns False.""" + return False diff --git a/tests/test_filter_parsing.py b/tests/test_filter_parsing.py new file mode 100644 index 0000000..c9129b3 --- /dev/null +++ b/tests/test_filter_parsing.py @@ -0,0 +1,242 @@ +"""Tests for Beacon v2 filter parsing functionality.""" + +import pytest + +from beacon_api.api.query_params import parse_filters_from_string + + +class TestJSONFilterParsing: + """Test JSON format filter parsing (POST requests).""" + + def test_single_ontology_filter_json(self): + """Test parsing a single ontology filter from JSON.""" + result = parse_filters_from_string('[{"id":"HP:0001250"}]') + assert len(result) == 1 + assert result[0].id == "HP:0001250" + assert result[0].operator is None + assert result[0].value is None + + def test_multiple_ontology_filters_json(self): + """Test parsing multiple ontology filters from JSON.""" + result = parse_filters_from_string('[{"id":"HP:0001250"},{"id":"NCIT:C6975"}]') + assert len(result) == 2 + assert result[0].id == "HP:0001250" + assert result[1].id == "NCIT:C6975" + + def test_alphanumeric_filter_json(self): + """Test parsing alphanumeric filter with operator and value.""" + result = parse_filters_from_string( + '[{"id":"PATO:0000011","operator":">","value":"P70Y"}]' + ) + assert len(result) == 1 + assert result[0].id == "PATO:0000011" + assert result[0].operator == ">" + assert result[0].value == "P70Y" + + def test_numeric_filter_json(self): + """Test parsing numeric filter with integer value.""" + result = parse_filters_from_string('[{"id":"age","operator":">=","value":18}]') + assert len(result) == 1 + assert result[0].id == "age" + assert result[0].operator == ">=" + assert result[0].value == 18 + + def test_mixed_filters_json(self): + """Test parsing mix of ontology and alphanumeric filters.""" + result = parse_filters_from_string( + '[{"id":"HP:0001250"},{"id":"PATO:0000011","operator":">","value":"P70Y"}]' + ) + assert len(result) == 2 + assert result[0].id == "HP:0001250" + assert result[0].operator is None + assert result[1].id == "PATO:0000011" + assert result[1].operator == ">" + assert result[1].value == "P70Y" + + def test_filter_with_include_descendant_terms(self): + """Test parsing filter with includeDescendantTerms.""" + result = parse_filters_from_string( + '[{"id":"HP:0001250","includeDescendantTerms":false}]' + ) + assert len(result) == 1 + assert result[0].id == "HP:0001250" + assert result[0].includeDescendantTerms is False + + def test_filter_with_similarity(self): + """Test parsing filter with similarity parameter.""" + result = parse_filters_from_string('[{"id":"HP:0001250","similarity":"high"}]') + assert len(result) == 1 + assert result[0].id == "HP:0001250" + assert result[0].similarity == "high" + + +class TestCommaSeparatedFilterParsing: + """Test comma-separated format filter parsing (GET requests).""" + + def test_single_ontology_filter_comma(self): + """Test parsing single ontology filter.""" + result = parse_filters_from_string("HP:0001250") + assert len(result) == 1 + assert result[0].id == "HP:0001250" + assert result[0].operator is None + + def test_multiple_ontology_filters_comma(self): + """Test parsing multiple comma-separated ontology filters.""" + result = parse_filters_from_string("HP:0001250,NCIT:C6975,HP:0100526") + assert len(result) == 3 + assert result[0].id == "HP:0001250" + assert result[1].id == "NCIT:C6975" + assert result[2].id == "HP:0100526" + + def test_ontology_filter_with_underscore(self): + """Test parsing filter with underscore instead of colon.""" + result = parse_filters_from_string("PATO_0000011") + assert len(result) == 1 + assert result[0].id == "PATO:0000011" # Underscore converted to colon + + def test_alphanumeric_filter_greater_than(self): + """Test parsing alphanumeric filter with > operator.""" + result = parse_filters_from_string("PATO_0000011:>P70Y") + assert len(result) == 1 + assert result[0].id == "PATO:0000011" + assert result[0].operator == ">" + assert result[0].value == "P70Y" + + def test_alphanumeric_filter_equals(self): + """Test parsing alphanumeric filter with = operator.""" + result = parse_filters_from_string("variant_type:=SNP") + assert len(result) == 1 + assert result[0].id == "variant:type" # Underscore converted + assert result[0].operator == "=" + assert result[0].value == "SNP" + + def test_numeric_filter_greater_than_equals(self): + """Test parsing numeric filter with >= operator.""" + result = parse_filters_from_string("age:>=18") + assert len(result) == 1 + assert result[0].id == "age" + assert result[0].operator == ">=" + assert result[0].value == 18 + assert isinstance(result[0].value, int) + + def test_numeric_filter_float_value(self): + """Test parsing numeric filter with float value.""" + result = parse_filters_from_string("score:>3.5") + assert len(result) == 1 + assert result[0].id == "score" + assert result[0].operator == ">" + assert result[0].value == 3.5 + assert isinstance(result[0].value, float) + + def test_mixed_filters_comma_separated(self): + """Test parsing mix of ontology and alphanumeric filters.""" + result = parse_filters_from_string("NCIT:C6975,PATO_0000011:>P70Y,HP:0001250") + assert len(result) == 3 + assert result[0].id == "NCIT:C6975" + assert result[0].operator is None + assert result[1].id == "PATO:0000011" + assert result[1].operator == ">" + assert result[1].value == "P70Y" + assert result[2].id == "HP:0001250" + assert result[2].operator is None + + def test_filter_with_not_operator(self): + """Test parsing filter with ! (NOT) operator.""" + result = parse_filters_from_string("status:!active") + assert len(result) == 1 + assert result[0].id == "status" + assert result[0].operator == "!" + assert result[0].value == "active" + + def test_filter_with_less_than(self): + """Test parsing filter with < operator.""" + result = parse_filters_from_string("age:<65") + assert len(result) == 1 + assert result[0].id == "age" + assert result[0].operator == "<" + assert result[0].value == 65 + + +class TestEdgeCases: + """Test edge cases and error handling.""" + + def test_empty_filter_string(self): + """Test parsing empty filter string returns None.""" + result = parse_filters_from_string("") + assert result is None + + def test_none_filter_string(self): + """Test parsing None filter string returns None.""" + result = parse_filters_from_string(None) + assert result is None + + def test_invalid_json_raises_error(self): + """Test that invalid JSON raises ValueError.""" + with pytest.raises(ValueError, match="Invalid JSON"): + parse_filters_from_string('[{"id":"HP:0001250"') + + def test_json_non_dict_array_raises_error(self): + """Test that JSON array of non-dicts raises ValueError.""" + with pytest.raises(ValueError, match="Invalid filter format"): + parse_filters_from_string('["string1", "string2"]') + + def test_whitespace_handling_comma_separated(self): + """Test that whitespace around commas is handled correctly.""" + result = parse_filters_from_string("HP:0001250 , NCIT:C6975 , HP:0100526") + assert len(result) == 3 + assert result[0].id == "HP:0001250" + assert result[1].id == "NCIT:C6975" + assert result[2].id == "HP:0100526" + + def test_empty_comma_segments_ignored(self): + """Test that empty segments between commas are ignored.""" + result = parse_filters_from_string("HP:0001250,,NCIT:C6975") + assert len(result) == 2 + assert result[0].id == "HP:0001250" + assert result[1].id == "NCIT:C6975" + + +class TestBeaconV2Examples: + """Test examples from Beacon v2 specification.""" + + def test_beacon_v2_ontology_example(self): + """Test ontology filter example from spec.""" + result = parse_filters_from_string('[{"id":"HP:0100526"}]') + assert len(result) == 1 + assert result[0].id == "HP:0100526" + + def test_beacon_v2_alphanumeric_example(self): + """Test alphanumeric filter example from spec.""" + result = parse_filters_from_string( + '[{"id":"PATO:0000011","operator":">","value":"P70Y"}]' + ) + assert len(result) == 1 + assert result[0].id == "PATO:0000011" + assert result[0].operator == ">" + assert result[0].value == "P70Y" + + def test_beacon_v2_multiple_filters_example(self): + """Test multiple filters example from spec.""" + result = parse_filters_from_string( + '[{"id":"NCIT:C6975"},{"id":"PATO:0000011","operator":">","value":"P70Y"}]' + ) + assert len(result) == 2 + assert result[0].id == "NCIT:C6975" + assert result[1].id == "PATO:0000011" + assert result[1].operator == ">" + assert result[1].value == "P70Y" + + def test_beacon_v2_get_format_simple(self): + """Test GET format simple filters from spec.""" + result = parse_filters_from_string("PMID:22824167,NCIT:C6975") + assert len(result) == 2 + assert result[0].id == "PMID:22824167" + assert result[1].id == "NCIT:C6975" + + def test_beacon_v2_get_format_with_operator(self): + """Test GET format with operator from spec.""" + result = parse_filters_from_string("PATO_0000011:>P70Y") + assert len(result) == 1 + assert result[0].id == "PATO:0000011" + assert result[0].operator == ">" + assert result[0].value == "P70Y" diff --git a/tests/test_info.py b/tests/test_info.py index 7c9b49e..617ec87 100644 --- a/tests/test_info.py +++ b/tests/test_info.py @@ -22,16 +22,17 @@ def test_get_beacon_info(client: TestClient) -> None: assert "meta" in data assert "response" in data - # Check meta structure + # Check meta structure (camelCase per Beacon v2 spec) meta = data["meta"] - assert "beacon_id" in meta - assert "api_version" in meta + assert "beaconId" in meta + assert "apiVersion" in meta + assert "returnedSchemas" in meta - # Check response structure + # Check response structure (camelCase per Beacon v2 spec) response_data = data["response"] assert "id" in response_data assert "name" in response_data - assert "api_version" in response_data + assert "apiVersion" in response_data assert "environment" in response_data assert "organization" in response_data diff --git a/tests/test_main.py b/tests/test_main.py index eba4caf..1a51d9d 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -25,9 +25,9 @@ def test_root_endpoint(client: TestClient) -> None: def test_health_check(client: TestClient) -> None: """Test health check endpoint.""" - response = client.get("/health") + response = client.get("/api/monitor/health") assert response.status_code == 200 - assert response.json() == {"status": "healthy"} + assert response.json() == {"status": "ok"} def test_openapi_schema(client: TestClient) -> None: @@ -42,6 +42,6 @@ def test_openapi_schema(client: TestClient) -> None: def test_docs_endpoint(client: TestClient) -> None: """Test interactive docs are accessible.""" - response = client.get("/docs") + response = client.get("/api/docs") assert response.status_code == 200 assert "text/html" in response.headers["content-type"] diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..6474854 --- /dev/null +++ b/uv.lock @@ -0,0 +1,932 @@ +version = 1 +revision = 2 +requires-python = ">=3.11" + +[[package]] +name = "annotated-types" +version = "0.7.0" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/ee/67/531ea369ba64dcff5ec9c3402f9f51bf748cec26dde048a2f973a4eea7f5/annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89", size = 16081, upload-time = "2024-05-20T21:33:25.928Z" } +wheels = [ + { url = 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