BioMCP

"""Comprehensive tests for network policies and HTTP centralization.""" from pathlib import Path from unittest.mock import patch import pytest from biomcp.http_client import request_api from biomcp.utils.endpoint_registry import ( DataType, EndpointCategory, EndpointInfo, EndpointRegistry, get_registry, ) class TestEndpointRegistry: """Test the endpoint registry functionality.""" def test_registry_initialization(self): """Test that registry initializes with known endpoints.""" registry = EndpointRegistry() endpoints = registry.get_all_endpoints() # Check we have endpoints registered assert len(endpoints) > 0 # Check specific endpoints exist assert "pubtator3_search" in endpoints assert "clinicaltrials_search" in endpoints assert "myvariant_query" in endpoints assert "cbioportal_api" in endpoints def test_get_endpoints_by_category(self): """Test filtering endpoints by category.""" registry = EndpointRegistry() # Get biomedical literature endpoints lit_endpoints = registry.get_endpoints_by_category( EndpointCategory.BIOMEDICAL_LITERATURE ) assert len(lit_endpoints) > 0 assert all( e.category == EndpointCategory.BIOMEDICAL_LITERATURE for e in lit_endpoints.values() ) # Get clinical trials endpoints trial_endpoints = registry.get_endpoints_by_category( EndpointCategory.CLINICAL_TRIALS ) assert len(trial_endpoints) > 0 assert all( e.category == EndpointCategory.CLINICAL_TRIALS for e in trial_endpoints.values() ) def test_get_unique_domains(self): """Test getting unique domains.""" registry = EndpointRegistry() domains = registry.get_unique_domains() assert len(domains) > 0 assert "www.ncbi.nlm.nih.gov" in domains assert "clinicaltrials.gov" in domains assert "myvariant.info" in domains assert "www.cbioportal.org" in domains def test_endpoint_info_properties(self): """Test EndpointInfo dataclass properties.""" endpoint = EndpointInfo( url="https://api.example.com/test", category=EndpointCategory.BIOMEDICAL_LITERATURE, data_types=[DataType.RESEARCH_ARTICLES], description="Test endpoint", compliance_notes="Test compliance", rate_limit="10 requests/second", authentication="API key required", ) assert endpoint.domain == "api.example.com" assert endpoint.category == EndpointCategory.BIOMEDICAL_LITERATURE assert DataType.RESEARCH_ARTICLES in endpoint.data_types def test_markdown_report_generation(self): """Test markdown report generation.""" registry = EndpointRegistry() report = registry.generate_markdown_report() # Check report contains expected sections assert "# Third-Party Endpoints Used by BioMCP" in report assert "## Overview" in report assert "## Endpoints by Category" in report assert "## Domain Summary" in report assert "## Compliance and Privacy" in report assert "## Network Control" in report # Check it mentions offline mode assert "BIOMCP_OFFLINE" in report # Check it contains actual endpoints assert "pubtator3" in report assert "clinicaltrials.gov" in report assert "myvariant.info" in report def test_save_markdown_report(self, tmp_path): """Test saving markdown report to file.""" registry = EndpointRegistry() output_path = tmp_path / "test_endpoints.md" saved_path = registry.save_markdown_report(output_path) assert saved_path == output_path assert output_path.exists() # Read and verify content content = output_path.read_text() assert "Third-Party Endpoints Used by BioMCP" in content class TestEndpointTracking: """Test endpoint tracking in HTTP client.""" @pytest.mark.asyncio async def test_valid_endpoint_key(self): """Test that valid endpoint keys are accepted.""" with patch("biomcp.http_client.call_http") as mock_call: mock_call.return_value = (200, '{"data": "test"}') # Should not raise an error result, error = await request_api( url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/", request={"text": "BRAF"}, endpoint_key="pubtator3_search", cache_ttl=0, ) assert result == {"data": "test"} assert error is None @pytest.mark.asyncio async def test_invalid_endpoint_key_raises_error(self): """Test that invalid endpoint keys raise an error.""" with pytest.raises(ValueError, match="Unknown endpoint key"): await request_api( url="https://api.example.com/test", request={"test": "data"}, endpoint_key="invalid_endpoint_key", cache_ttl=0, ) @pytest.mark.asyncio async def test_no_endpoint_key_allowed(self): """Test that requests without endpoint keys are allowed.""" with patch("biomcp.http_client.call_http") as mock_call: mock_call.return_value = (200, '{"data": "test"}') # Should not raise an error result, error = await request_api( url="https://api.example.com/test", request={"test": "data"}, cache_ttl=0, ) assert result == {"data": "test"} assert error is None class TestHTTPImportChecks: """Test the HTTP import checking script.""" def test_check_script_exists(self): """Test that the check script exists.""" script_path = ( Path(__file__).parent.parent.parent / "scripts" / "check_http_imports.py" ) assert script_path.exists() def test_allowed_files_configured(self): """Test that allowed files are properly configured.""" # Import the script module import sys script_path = Path(__file__).parent.parent.parent / "scripts" sys.path.insert(0, str(script_path)) try: from check_http_imports import ALLOWED_FILES, HTTP_LIBRARIES # Check essential files are allowed assert "http_client.py" in ALLOWED_FILES assert "http_client_simple.py" in ALLOWED_FILES # Check we're checking for the right libraries assert "httpx" in HTTP_LIBRARIES assert "aiohttp" in HTTP_LIBRARIES assert "requests" in HTTP_LIBRARIES finally: sys.path.pop(0) class TestGlobalRegistry: """Test the global registry instance.""" def test_get_registry_returns_same_instance(self): """Test that get_registry returns the same instance.""" registry1 = get_registry() registry2 = get_registry() assert registry1 is registry2 def test_global_registry_has_endpoints(self): """Test that the global registry has endpoints.""" registry = get_registry() endpoints = registry.get_all_endpoints() assert len(endpoints) > 0