CEDAR MCP Server

#!/usr/bin/env python3 import pytest from typing import Dict from src.cedar_mcp.external_api import ( get_children_from_branch, search_instance_ids, get_instance, ) @pytest.mark.integration class TestGetChildrenFromBranch: """Integration tests for get_children_from_branch function.""" def test_get_children_valid_branch( self, bioportal_api_key: str, sample_bioportal_branch: Dict[str, str] ): """Test fetching children from a valid BioPortal branch.""" branch_iri = sample_bioportal_branch["branch_iri"] ontology_acronym = sample_bioportal_branch["ontology_acronym"] result = get_children_from_branch( branch_iri, ontology_acronym, bioportal_api_key ) # Should not contain error assert "error" not in result # Should have collection with children assert "collection" in result assert isinstance(result["collection"], list) # If there are children, they should have required fields if result["collection"]: child = result["collection"][0] assert "@id" in child assert "prefLabel" in child assert isinstance(child["prefLabel"], str) assert child["prefLabel"].strip() != "" def test_get_children_invalid_branch_iri(self, bioportal_api_key: str): """Test fetching children with invalid branch IRI.""" invalid_iri = "http://invalid.example.com/nonexistent" ontology_acronym = "HRAVS" result = get_children_from_branch( invalid_iri, ontology_acronym, bioportal_api_key ) # Should return error for invalid IRI assert "error" in result assert "Failed to fetch children from BioPortal" in result["error"] def test_get_children_invalid_ontology(self, bioportal_api_key: str): """Test fetching children with invalid ontology acronym.""" branch_iri = "http://purl.obolibrary.org/obo/CHEBI_23367" invalid_ontology = "NONEXISTENT_ONTOLOGY" result = get_children_from_branch( branch_iri, invalid_ontology, bioportal_api_key ) # Should return error for invalid ontology assert "error" in result assert "Failed to fetch children from BioPortal" in result["error"] def test_get_children_invalid_api_key( self, sample_bioportal_branch: Dict[str, str] ): """Test fetching children with invalid API key.""" branch_iri = sample_bioportal_branch["branch_iri"] ontology_acronym = sample_bioportal_branch["ontology_acronym"] invalid_api_key = "invalid-api-key-12345" result = get_children_from_branch(branch_iri, ontology_acronym, invalid_api_key) # Should return error for invalid API key assert "error" in result assert "Failed to fetch children from BioPortal" in result["error"] def test_get_children_empty_parameters(self, bioportal_api_key: str): """Test fetching children with empty parameters.""" result = get_children_from_branch("", "CHEBI", bioportal_api_key) assert "error" in result result = get_children_from_branch( "http://example.com/test", "", bioportal_api_key ) assert "error" in result def test_get_children_url_encoding(self, bioportal_api_key: str): """Test that special characters in IRI are properly URL encoded.""" # Use IRI with special characters that need encoding branch_iri = "http://purl.obolibrary.org/obo/CHEBI_23367#special chars" ontology_acronym = "CHEBI" result = get_children_from_branch( branch_iri, ontology_acronym, bioportal_api_key ) # Should handle URL encoding without raising exceptions # Result may be error (invalid IRI) but should not crash assert isinstance(result, dict) assert "error" in result or "collection" in result @pytest.mark.slow def test_get_children_response_structure(self, bioportal_api_key: str): """Test detailed response structure from BioPortal API.""" # Use a known branch that should have children branch_iri = "http://purl.obolibrary.org/obo/CHEBI_23367" ontology_acronym = "CHEBI" result = get_children_from_branch( branch_iri, ontology_acronym, bioportal_api_key ) if "error" not in result: # Verify BioPortal response structure assert "collection" in result # If there are children, verify their structure if result["collection"]: for child in result["collection"]: assert isinstance(child, dict) assert "@id" in child assert "prefLabel" in child # Verify IRI format assert child["@id"].startswith("http") # Verify prefLabel is non-empty string assert isinstance(child["prefLabel"], str) assert len(child["prefLabel"].strip()) > 0 def test_get_children_multiple_ontologies(self, bioportal_api_key: str): """Test fetching children from different ontologies.""" test_cases = [ { "branch_iri": "http://purl.obolibrary.org/obo/CHEBI_23367", "ontology_acronym": "CHEBI", } # Add more test cases here if you have access to other ontologies ] for case in test_cases: result = get_children_from_branch( case["branch_iri"], case["ontology_acronym"], bioportal_api_key ) # Should return valid response (either data or reasonable error) assert isinstance(result, dict) assert "error" in result or "collection" in result @pytest.mark.unit class TestSearchInstanceIds: """Tests for search_instance_ids function.""" def test_search_instances_basic_functionality(self, cedar_api_key: str): """Test basic search functionality.""" template_id = "8b47bae6-db32-4b13-9d12-d012f0be9412" result = search_instance_ids(template_id, cedar_api_key, limit=2) # Should have expected structure assert "instance_ids" in result assert "pagination" in result assert isinstance(result["instance_ids"], list) assert isinstance(result["pagination"], dict) # Check pagination metadata structure pagination = result["pagination"] assert "total_count" in pagination assert "limit" in pagination assert "offset" in pagination assert "current_page" in pagination assert "total_pages" in pagination assert "has_next" in pagination assert isinstance(pagination["total_count"], int) # Should have found instances (this template has many) if "error" not in result: assert pagination["total_count"] > 0 def test_search_instances_invalid_api_key(self): """Test search with invalid API key.""" result = search_instance_ids( "8b47bae6-db32-4b13-9d12-d012f0be9412", "invalid-key", limit=2 ) assert "error" in result @pytest.mark.unit class TestGetInstance: """Tests for get_instance function.""" def test_get_instance_invalid_api_key(self): """Test fetching instance with invalid API key.""" instance_id = "https://repo.metadatacenter.org/template-instances/test-id" result = get_instance(instance_id, "invalid-api-key") assert "error" in result