BioMCP

"""Tests for variant getter module.""" from unittest.mock import AsyncMock, patch import pytest from biomcp.constants import DEFAULT_ASSEMBLY from biomcp.variants import getter class TestGetVariant: """Test the get_variant function.""" @pytest.mark.asyncio async def test_get_variant_default_assembly(self): """Test that get_variant defaults to hg19 assembly.""" mock_response = { "_id": "rs113488022", "dbsnp": {"rsid": "rs113488022"}, } with patch("biomcp.http_client.request_api") as mock_request: mock_request.return_value = (mock_response, None) await getter.get_variant("rs113488022") # Verify assembly parameter was passed with default value call_args = mock_request.call_args assert call_args[1]["request"]["assembly"] == "hg19" @pytest.mark.asyncio async def test_get_variant_hg38_assembly(self): """Test that get_variant accepts hg38 assembly parameter.""" mock_response = { "_id": "rs113488022", "dbsnp": {"rsid": "rs113488022"}, } with patch("biomcp.http_client.request_api") as mock_request: mock_request.return_value = (mock_response, None) await getter.get_variant("rs113488022", assembly="hg38") # Verify assembly parameter was passed correctly call_args = mock_request.call_args assert call_args[1]["request"]["assembly"] == "hg38" @pytest.mark.asyncio async def test_get_variant_hg19_assembly(self): """Test that get_variant accepts hg19 assembly parameter explicitly.""" mock_response = { "_id": "rs113488022", "dbsnp": {"rsid": "rs113488022"}, } with patch("biomcp.http_client.request_api") as mock_request: mock_request.return_value = (mock_response, None) await getter.get_variant("rs113488022", assembly="hg19") # Verify assembly parameter was passed correctly call_args = mock_request.call_args assert call_args[1]["request"]["assembly"] == "hg19" @pytest.mark.asyncio async def test_get_variant_includes_all_fields(self): """Test that request includes all required fields.""" mock_response = {"_id": "rs113488022"} with patch("biomcp.http_client.request_api") as mock_request: mock_request.return_value = (mock_response, None) await getter.get_variant("rs113488022", assembly="hg38") # Verify both fields and assembly are in request call_args = mock_request.call_args request_params = call_args[1]["request"] assert "fields" in request_params assert request_params["fields"] == "all" assert "assembly" in request_params assert request_params["assembly"] == "hg38" @pytest.mark.asyncio async def test_get_variant_with_external_annotations(self): """Test that assembly parameter works with external annotations.""" from biomcp.variants.external import EnhancedVariantAnnotation mock_response = { "_id": "rs113488022", "dbsnp": {"rsid": "rs113488022"}, "dbnsfp": {"genename": "BRAF"}, } with ( patch("biomcp.http_client.request_api") as mock_request, patch( "biomcp.variants.getter.ExternalVariantAggregator" ) as mock_aggregator, ): mock_request.return_value = (mock_response, None) # Mock the aggregator with proper EnhancedVariantAnnotation mock_enhanced = EnhancedVariantAnnotation( variant_id="rs113488022", tcga=None, thousand_genomes=None, cbioportal=None, error_sources=[], ) mock_agg_instance = AsyncMock() mock_agg_instance.get_enhanced_annotations = AsyncMock( return_value=mock_enhanced ) mock_aggregator.return_value = mock_agg_instance await getter.get_variant( "rs113488022", assembly="hg38", include_external=True, ) # Verify assembly was still passed correctly call_args = mock_request.call_args assert call_args[1]["request"]["assembly"] == "hg38" class TestVariantDetailsMCPTool: """Test the _variant_details MCP tool.""" @pytest.mark.asyncio async def test_variant_details_default_assembly(self): """Test that _variant_details defaults to hg19 assembly.""" with patch("biomcp.variants.getter.get_variant") as mock_get: mock_get.return_value = "Variant details" await getter._variant_details( call_benefit="Testing default assembly", variant_id="rs113488022", ) # Verify get_variant was called with default assembly mock_get.assert_called_once_with( "rs113488022", output_json=False, include_external=True, assembly=DEFAULT_ASSEMBLY, ) @pytest.mark.asyncio async def test_variant_details_custom_assembly(self): """Test that _variant_details accepts custom assembly parameter.""" with patch("biomcp.variants.getter.get_variant") as mock_get: mock_get.return_value = "Variant details" await getter._variant_details( call_benefit="Testing hg38 assembly", variant_id="rs113488022", assembly="hg38", ) # Verify get_variant was called with hg38 mock_get.assert_called_once_with( "rs113488022", output_json=False, include_external=True, assembly="hg38", ) @pytest.mark.asyncio async def test_variant_details_with_all_params(self): """Test that all parameters are passed through correctly.""" with patch("biomcp.variants.getter.get_variant") as mock_get: mock_get.return_value = "Variant details" await getter._variant_details( call_benefit="Testing all parameters", variant_id="chr7:g.140453136A>T", include_external=False, assembly="hg19", ) # Verify all params were passed mock_get.assert_called_once_with( "chr7:g.140453136A>T", output_json=False, include_external=False, assembly="hg19", )