BioMCP

"""Integration tests for BioThings API - calls real APIs.""" import pytest from biomcp.integrations import BioThingsClient @pytest.mark.integration class TestRealBioThingsAPIs: """Integration tests that call real BioThings APIs.""" @pytest.fixture def client(self): """Create a real BioThings client.""" return BioThingsClient() @pytest.mark.asyncio async def test_mygene_tp53(self, client): """Test real MyGene.info API with TP53.""" result = await client.get_gene_info("TP53") assert result is not None assert result.symbol == "TP53" assert result.name == "tumor protein p53" assert result.entrezgene in ["7157", 7157] assert "tumor suppressor" in result.summary.lower() # Check for either lowercase or uppercase P53 in aliases assert any("p53" in alias.lower() for alias in result.alias) @pytest.mark.asyncio async def test_mygene_braf(self, client): """Test real MyGene.info API with BRAF.""" result = await client.get_gene_info("BRAF") assert result is not None assert result.symbol == "BRAF" assert "proto-oncogene" in result.name.lower() assert result.type_of_gene == "protein-coding" @pytest.mark.asyncio async def test_mygene_by_entrez_id(self, client): """Test real MyGene.info API with Entrez ID.""" result = await client.get_gene_info("673") # BRAF assert result is not None assert result.symbol == "BRAF" assert result.gene_id == "673" @pytest.mark.asyncio async def test_mydisease_melanoma(self, client): """Test real MyDisease.info API with melanoma.""" result = await client.get_disease_info("melanoma") if result is None: # API might be down or melanoma might not be found directly # Try a more specific search result = await client.get_disease_info( "MONDO:0005105" ) # MONDO ID for melanoma assert result is not None, "Disease info should be returned" # The API may return subtypes of melanoma if result.name: assert "melanoma" in result.name.lower() or ( result.definition and "melanoma" in result.definition.lower() ) assert result.disease_id is not None # Synonyms might be empty for specific subtypes assert result.synonyms is not None @pytest.mark.asyncio async def test_mydisease_gist(self, client): """Test real MyDisease.info API with GIST.""" result = await client.get_disease_info("GIST") if result is None: # API might be down or GIST might not be found directly # Try the full name result = await client.get_disease_info( "gastrointestinal stromal tumor" ) assert result is not None, "Disease info should be returned" # GIST might return as a variant name if result.name: assert ( "gist" in result.name.lower() or "stromal" in result.name.lower() ) assert result.disease_id is not None # GIST should have synonyms including full name if available assert result.synonyms is not None @pytest.mark.asyncio async def test_mydisease_by_mondo_id(self, client): """Test real MyDisease.info API with MONDO ID.""" result = await client.get_disease_info("MONDO:0005105") # melanoma assert result is not None assert result.disease_id == "MONDO:0005105" # The result should have mondo data assert result.mondo is not None assert result.mondo.get("mondo") == "MONDO:0005105" # Name field might come from different sources in the API if result.name: assert "melanoma" in result.name.lower() @pytest.mark.asyncio async def test_disease_synonyms_expansion(self, client): """Test disease synonym expansion.""" synonyms = await client.get_disease_synonyms("lung cancer") assert len(synonyms) >= 1 # At least includes the original term assert "lung cancer" in [s.lower() for s in synonyms] # May or may not include formal terms depending on API results # Just check we got some results back assert synonyms is not None and len(synonyms) > 0 @pytest.mark.asyncio async def test_batch_genes(self, client): """Test batch gene retrieval.""" # Test single gene retrieval as a workaround since batch requires special POST encoding # This validates the gene getter can handle multiple calls efficiently genes = ["TP53", "BRAF", "EGFR"] results = [] for gene in genes: result = await client.get_gene_info(gene) if result: results.append(result) assert len(results) == 3 gene_symbols = [r.symbol for r in results] assert "TP53" in gene_symbols assert "BRAF" in gene_symbols assert "EGFR" in gene_symbols @pytest.mark.asyncio async def test_invalid_gene(self, client): """Test handling of invalid gene.""" result = await client.get_gene_info("INVALID_GENE_XYZ123") assert result is None @pytest.mark.asyncio async def test_invalid_disease(self, client): """Test handling of invalid disease.""" result = await client.get_disease_info("INVALID_DISEASE_XYZ123") assert result is None @pytest.mark.asyncio async def test_mychem_aspirin(self, client): """Test real MyChem.info API with aspirin.""" # Use DrugBank ID for reliable results result = await client.get_drug_info("DB00945") assert result is not None # API returns various forms - could be aspirin or acetylsalicylic acid assert result.name is not None assert result.drugbank_id == "DB00945" # Should have at least one identifier assert any([ result.drugbank_id, result.chembl_id, result.chebi_id, result.pubchem_cid, ]) @pytest.mark.asyncio async def test_mychem_imatinib(self, client): """Test real MyChem.info API with imatinib.""" # Use DrugBank ID for reliable results result = await client.get_drug_info("DB00619") assert result is not None assert result.name is not None assert "imatinib" in result.name.lower() assert result.drugbank_id == "DB00619" # Should have at least one identifier assert any([ result.drugbank_id, result.chembl_id, result.chebi_id, result.pubchem_cid, ]) @pytest.mark.asyncio async def test_mychem_by_drugbank_id(self, client): """Test real MyChem.info API with DrugBank ID.""" result = await client.get_drug_info("DB00945") # Aspirin assert result is not None assert result.drugbank_id == "DB00945" assert ( result.name is not None ) # Could be Acetylsalicylic acid or similar @pytest.mark.asyncio async def test_invalid_drug(self, client): """Test handling of invalid drug.""" result = await client.get_drug_info("INVALID_DRUG_XYZ123") assert result is None @pytest.mark.asyncio async def test_mychem_pembrolizumab(self, client): """Test real MyChem.info API with pembrolizumab.""" result = await client.get_drug_info("pembrolizumab") assert result is not None assert result.name == "Pembrolizumab" assert result.drugbank_id == "DB09037" assert result.unii == "DPT0O3T46P" assert "PD-1" in result.description assert "antibody" in result.description.lower() @pytest.mark.integration class TestGeneToolIntegration: """Test the gene getter tool with real APIs.""" @pytest.mark.asyncio async def test_gene_getter_tool(self): """Test the gene_getter tool function.""" from biomcp.genes.getter import get_gene result = await get_gene("TP53", output_json=False) assert "TP53" in result assert "tumor protein p53" in result assert "tumor suppressor" in result.lower() # Links might be formatted differently assert "ncbi" in result.lower() or "gene" in result.lower() @pytest.mark.asyncio async def test_gene_getter_json(self): """Test gene_getter with JSON output.""" import json from biomcp.genes.getter import get_gene result = await get_gene("BRAF", output_json=True) data = json.loads(result) assert data["symbol"] == "BRAF" assert "_links" in data assert "NCBI Gene" in data["_links"] @pytest.mark.integration class TestDiseaseToolIntegration: """Test the disease getter tool with real APIs.""" @pytest.mark.asyncio async def test_disease_getter_tool(self): """Test the disease_getter tool function.""" from biomcp.diseases.getter import get_disease result = await get_disease("melanoma", output_json=False) assert "melanoma" in result.lower() assert "MONDO:" in result # In markdown format, links are shown as "MONDO Browser:" not "_links" assert "Browser:" in result or "https://" in result @pytest.mark.asyncio async def test_disease_getter_json(self): """Test disease_getter with JSON output.""" import json from biomcp.diseases.getter import get_disease result = await get_disease("GIST", output_json=True) data = json.loads(result) # API might return error or different structure if "error" in data: pytest.skip("Disease not found in API") else: # Check for key fields assert "disease_id" in data or "id" in data or "_id" in data assert "MONDO:" in str(data) @pytest.mark.integration class TestDrugToolIntegration: """Test the drug getter tool with real APIs.""" @pytest.mark.asyncio async def test_drug_getter_tool(self): """Test the drug_getter tool function.""" from biomcp.drugs.getter import get_drug result = await get_drug("DB00945", output_json=False) # Aspirin assert "Drug:" in result assert "DrugBank ID" in result assert "DB00945" in result assert "External Links" in result @pytest.mark.asyncio async def test_drug_getter_json(self): """Test drug_getter with JSON output.""" import json from biomcp.drugs.getter import get_drug result = await get_drug("DB00619", output_json=True) # Imatinib data = json.loads(result) # Check for basic fields assert "drug_id" in data assert "drugbank_id" in data assert data["drugbank_id"] == "DB00619" assert "_links" in data # Should have at least one database link assert any( key in data["_links"] for key in ["DrugBank", "ChEMBL", "PubChem", "ChEBI"] )