BioMCP

"""Unit tests for NCI CTS API integration.""" from unittest.mock import patch import pytest from biomcp.biomarkers import search_biomarkers from biomcp.diseases.search import search_diseases from biomcp.integrations.cts_api import CTSAPIError, make_cts_request from biomcp.interventions import search_interventions from biomcp.organizations import get_organization, search_organizations from biomcp.trials.nci_getter import get_trial_nci from biomcp.trials.nci_search import convert_query_to_nci, search_trials_nci from biomcp.trials.search import TrialQuery class TestCTSAPIIntegration: """Test CTS API helper functions.""" @pytest.mark.asyncio async def test_make_cts_request_no_api_key(self): """Test that missing API key raises appropriate error.""" with ( patch.dict("os.environ", {}, clear=True), pytest.raises(CTSAPIError, match="NCI API key required"), ): await make_cts_request("https://example.com/api") @pytest.mark.asyncio async def test_make_cts_request_with_api_key(self): """Test successful request with API key.""" with patch("biomcp.integrations.cts_api.request_api") as mock_request: mock_request.return_value = ({"data": "test"}, None) result = await make_cts_request( "https://example.com/api", api_key="test-key" ) assert result == {"data": "test"} mock_request.assert_called_once() # Verify headers were included call_args = mock_request.call_args request_data = call_args.kwargs["request"] assert "_headers" in request_data class TestOrganizationsModule: """Test organizations module functions.""" @pytest.mark.asyncio async def test_search_organizations(self): """Test organization search.""" with patch( "biomcp.organizations.search.make_cts_request" ) as mock_request: mock_request.return_value = { "data": [{"id": "ORG001", "name": "Test Cancer Center"}], "total": 1, } result = await search_organizations( name="Cancer Center", api_key="test-key" ) assert result["total"] == 1 assert len(result["organizations"]) == 1 assert result["organizations"][0]["name"] == "Test Cancer Center" @pytest.mark.asyncio async def test_get_organization(self): """Test getting specific organization.""" with patch( "biomcp.organizations.getter.make_cts_request" ) as mock_request: mock_request.return_value = { "data": { "id": "ORG001", "name": "Test Cancer Center", "type": "Academic", } } result = await get_organization("ORG001", api_key="test-key") assert result["id"] == "ORG001" assert result["name"] == "Test Cancer Center" assert result["type"] == "Academic" class TestInterventionsModule: """Test interventions module functions.""" @pytest.mark.asyncio async def test_search_interventions(self): """Test intervention search.""" with patch( "biomcp.interventions.search.make_cts_request" ) as mock_request: mock_request.return_value = { "data": [ {"id": "INT001", "name": "Pembrolizumab", "type": "Drug"} ], "total": 1, } result = await search_interventions( name="Pembrolizumab", api_key="test-key" ) assert result["total"] == 1 assert len(result["interventions"]) == 1 assert result["interventions"][0]["name"] == "Pembrolizumab" class TestBiomarkersModule: """Test biomarkers module functions.""" @pytest.mark.asyncio async def test_search_biomarkers(self): """Test biomarker search.""" with patch( "biomcp.biomarkers.search.make_cts_request" ) as mock_request: mock_request.return_value = { "data": [{"id": "BIO001", "name": "PD-L1", "gene": "CD274"}], "total": 1, } result = await search_biomarkers(name="PD-L1", api_key="test-key") assert result["total"] == 1 assert len(result["biomarkers"]) == 1 assert result["biomarkers"][0]["name"] == "PD-L1" class TestDiseasesModule: """Test diseases module functions.""" @pytest.mark.asyncio async def test_search_diseases_nci(self): """Test disease search via NCI API.""" with patch("biomcp.diseases.search.make_cts_request") as mock_request: mock_request.return_value = { "data": [ { "id": "DIS001", "name": "Melanoma", "synonyms": ["Malignant Melanoma"], } ], "total": 1, } result = await search_diseases(name="Melanoma", api_key="test-key") assert result["total"] == 1 assert len(result["diseases"]) == 1 assert result["diseases"][0]["name"] == "Melanoma" class TestNCITrialIntegration: """Test NCI trial search and getter.""" @pytest.mark.asyncio async def test_convert_query_to_nci(self): """Test converting TrialQuery to NCI parameters.""" query = TrialQuery( conditions=["melanoma"], phase="PHASE2", recruiting_status="OPEN", allow_brain_mets=True, ) # Mock the disease/intervention lookups with ( patch("biomcp.trials.nci_search.search_diseases") as mock_diseases, patch( "biomcp.trials.nci_search.search_interventions" ) as mock_interventions, ): mock_diseases.return_value = {"diseases": []} mock_interventions.return_value = {"interventions": []} params = await convert_query_to_nci(query) assert params["diseases"] == ["melanoma"] assert params["phase"] == "II" assert params["recruitment_status"] == [ "recruiting", "enrolling_by_invitation", ] assert params["accepts_brain_mets"] is True @pytest.mark.asyncio async def test_search_trials_nci(self): """Test NCI trial search.""" query = TrialQuery(conditions=["melanoma"]) with ( patch( "biomcp.trials.nci_search.convert_query_to_nci" ) as mock_convert, patch("biomcp.trials.nci_search.make_cts_request") as mock_request, ): mock_convert.return_value = {"diseases": ["melanoma"]} mock_request.return_value = { "data": [ { "nct_id": "NCT12345", "title": "Test Trial", "phase": "II", } ], "total": 1, } result = await search_trials_nci(query, api_key="test-key") assert result["total"] == 1 assert result["source"] == "nci" assert len(result["trials"]) == 1 assert result["trials"][0]["nct_id"] == "NCT12345" @pytest.mark.asyncio async def test_get_trial_nci(self): """Test getting specific trial from NCI.""" with patch( "biomcp.trials.nci_getter.make_cts_request" ) as mock_request: mock_request.return_value = { "data": { "nct_id": "NCT12345", "title": "Test Trial", "phase": "II", "overall_status": "Recruiting", } } result = await get_trial_nci("NCT12345", api_key="test-key") assert result["nct_id"] == "NCT12345" assert result["title"] == "Test Trial" assert result["phase"] == "II"