BioMCP

"""Test cBioPortal integration with article searches.""" import json import pytest from biomcp.articles.search import PubmedRequest from biomcp.articles.unified import search_articles_unified class TestArticleCBioPortalIntegration: """Test that cBioPortal summaries appear in article searches.""" @pytest.mark.asyncio @pytest.mark.integration async def test_article_search_with_gene_includes_cbioportal(self): """Test that searching articles for a gene includes cBioPortal summary.""" request = PubmedRequest( genes=["BRAF"], keywords=["melanoma"], ) # Test markdown output result = await search_articles_unified( request, include_pubmed=True, include_preprints=False, output_json=False, ) # Should include cBioPortal summary assert "cBioPortal Summary for BRAF" in result assert "Mutation Frequency" in result # Top Hotspots is only included when mutations are found # When cBioPortal API returns empty data, it won't be present if "0.0%" not in result: # If mutation frequency is not 0 assert "Top Hotspots" in result assert "---" in result # Separator between summary and articles # Should still include article results assert "pmid" in result or "Title" in result or "Record" in result @pytest.mark.asyncio @pytest.mark.integration async def test_article_search_json_with_gene(self): """Test JSON output includes cBioPortal summary.""" request = PubmedRequest( genes=["TP53"], keywords=["cancer"], ) result = await search_articles_unified( request, include_pubmed=True, include_preprints=False, output_json=True, ) # Parse JSON data = json.loads(result) # Should have both summary and articles assert "cbioportal_summary" in data assert "articles" in data assert "TP53" in data["cbioportal_summary"] assert isinstance(data["articles"], list) assert len(data["articles"]) > 0 @pytest.mark.asyncio @pytest.mark.integration async def test_article_search_without_gene_no_cbioportal(self): """Test that searches without genes don't include cBioPortal summary.""" request = PubmedRequest( diseases=["hypertension"], keywords=["treatment"], ) # Test markdown output result = await search_articles_unified( request, include_pubmed=True, include_preprints=False, output_json=False, ) # Should NOT include cBioPortal summary assert "cBioPortal Summary" not in result assert "Mutation Frequency" not in result @pytest.mark.asyncio @pytest.mark.integration async def test_article_search_multiple_genes(self): """Test that searching with multiple genes uses the first one.""" request = PubmedRequest( genes=["KRAS", "NRAS", "BRAF"], diseases=["colorectal cancer"], ) result = await search_articles_unified( request, include_pubmed=True, include_preprints=False, output_json=False, ) # Should include cBioPortal summary for KRAS (first gene) assert "cBioPortal Summary for KRAS" in result # Common KRAS hotspot assert "G12" in result or "mutation" in result @pytest.mark.asyncio @pytest.mark.integration async def test_article_search_with_invalid_gene(self): """Test graceful handling of invalid gene names.""" request = PubmedRequest( genes=["BRCA1"], # Valid gene keywords=["cancer"], ) # First check that we handle invalid genes gracefully # by using a real gene that might have cBioPortal data result = await search_articles_unified( request, include_pubmed=True, include_preprints=False, output_json=False, ) # Should have some content - either cBioPortal summary or articles assert len(result) > 50 # Some reasonable content # Now test with a gene that's valid for search but not in cBioPortal request2 = PubmedRequest( genes=["ACE2"], # Real gene but might not be in cancer studies keywords=["COVID-19"], ) result2 = await search_articles_unified( request2, include_pubmed=True, include_preprints=False, output_json=False, ) # Should return results even if cBioPortal data is not available assert len(result2) > 50 @pytest.mark.asyncio @pytest.mark.integration async def test_article_search_with_preprints_and_cbioportal(self): """Test that cBioPortal summary works with preprint searches too.""" request = PubmedRequest( genes=["EGFR"], keywords=["lung cancer", "osimertinib"], ) result = await search_articles_unified( request, include_pubmed=True, include_preprints=True, output_json=False, ) # Should include cBioPortal summary assert "cBioPortal Summary for EGFR" in result # Should include both peer-reviewed and preprint results assert ("pmid" in result or "Title" in result) and ( "Preprint" in result or "bioRxiv" in result or "peer_reviewed" in result )