BioMCP

"""Tests for AlphaGenome integration.""" from unittest.mock import patch import pytest from biomcp.variants.alphagenome import predict_variant_effects @pytest.mark.asyncio async def test_predict_variant_effects_no_api_key(): """Test that missing API key returns helpful error message.""" with patch.dict("os.environ", {}, clear=True): result = await predict_variant_effects( chromosome="chr7", position=140753336, reference="A", alternate="T", ) assert "AlphaGenome API key required" in result assert "https://deepmind.google.com/science/alphagenome" in result assert "ALPHAGENOME_API_KEY" in result @pytest.mark.asyncio async def test_predict_variant_effects_not_installed(): """Test that missing AlphaGenome package returns installation instructions or API error.""" # Since AlphaGenome might be installed in test environments, we need to test both cases # We'll set a dummy API key and check what error we get import os original_key = os.environ.get("ALPHAGENOME_API_KEY") try: os.environ["ALPHAGENOME_API_KEY"] = "test-key" result = await predict_variant_effects( chromosome="chr7", position=140753336, reference="A", alternate="T", skip_cache=True, # Skip cache to ensure fresh results ) # The function should either: # 1. Handle ImportError if AlphaGenome is not installed # 2. Return API error if AlphaGenome is installed but API key is invalid # 3. Return a prediction failure for other errors assert any([ "AlphaGenome not installed" in result, "AlphaGenome prediction failed" in result, "API key not valid" in result, # This can happen with invalid test keys ]) if "AlphaGenome not installed" in result: assert "git clone" in result assert "pip install" in result finally: # Restore original key if original_key is None: os.environ.pop("ALPHAGENOME_API_KEY", None) else: os.environ["ALPHAGENOME_API_KEY"] = original_key @pytest.mark.asyncio async def test_predict_variant_effects_basic_parameters(): """Test that function accepts the expected parameters.""" # This tests the function interface without requiring AlphaGenome with patch.dict("os.environ", {}, clear=True): # Test with all parameters result = await predict_variant_effects( chromosome="chrX", position=12345, reference="G", alternate="C", interval_size=500_000, tissue_types=["UBERON:0002367", "UBERON:0001157"], ) # Should get API key error (not import error), proving parameters were accepted assert "AlphaGenome API key required" in result