test_cancer_at_home.py

"""
Test Suite for Cancer@Home v2
Run with: pytest test_cancer_at_home.py
"""

import pytest
from pathlib import Path


class TestConfiguration:
    """Test configuration file"""
    
    def test_config_exists(self):
        """Check if config file exists"""
        assert Path("config.yml").exists()
    
    def test_requirements_exists(self):
        """Check if requirements file exists"""
        assert Path("requirements.txt").exists()


class TestBOINC:
    """Test BOINC integration"""
    
    def test_boinc_client_import(self):
        """Test BOINC client can be imported"""
        from backend.boinc import BOINCClient
        assert BOINCClient is not None
    
    def test_boinc_task_submission(self):
        """Test task submission"""
        from backend.boinc import BOINCClient
        
        client = BOINCClient()
        task_id = client.submit_task("test_task", "test_input.txt")
        
        assert task_id is not None
        assert task_id.startswith("wu_")
        
        # Check task exists
        task = client.get_task_status(task_id)
        assert task is not None
        assert task.status == "pending"


class TestGDC:
    """Test GDC integration"""
    
    def test_gdc_client_import(self):
        """Test GDC client can be imported"""
        from backend.gdc import GDCClient
        assert GDCClient is not None
    
    def test_gdc_client_initialization(self):
        """Test GDC client initialization"""
        from backend.gdc import GDCClient
        
        client = GDCClient()
        assert client.api_url == "https://api.gdc.cancer.gov"


class TestPipeline:
    """Test bioinformatics pipeline"""
    
    def test_fastq_processor_import(self):
        """Test FASTQ processor import"""
        from backend.pipeline import FASTQProcessor
        assert FASTQProcessor is not None
    
    def test_blast_runner_import(self):
        """Test BLAST runner import"""
        from backend.pipeline import BLASTRunner
        assert BLASTRunner is not None
    
    def test_variant_caller_import(self):
        """Test variant caller import"""
        from backend.pipeline import VariantCaller
        assert VariantCaller is not None


class TestNeo4j:
    """Test Neo4j integration"""
    
    def test_db_manager_import(self):
        """Test database manager import"""
        from backend.neo4j import DatabaseManager
        assert DatabaseManager is not None
    
    def test_repositories_import(self):
        """Test repository imports"""
        from backend.neo4j import (
            GeneRepository,
            MutationRepository,
            PatientRepository,
            CancerTypeRepository
        )
        
        assert GeneRepository is not None
        assert MutationRepository is not None
        assert PatientRepository is not None
        assert CancerTypeRepository is not None


class TestAPI:
    """Test API endpoints"""
    
    def test_api_import(self):
        """Test API can be imported"""
        from backend.api import app
        assert app is not None
    
    def test_api_title(self):
        """Test API metadata"""
        from backend.api import app
        assert app.title == "Cancer@Home v2"
        assert app.version == "2.0.0"


class TestDirectoryStructure:
    """Test directory structure"""
    
    def test_backend_exists(self):
        """Check backend directory"""
        assert Path("backend").exists()
        assert Path("backend/__init__.py").exists()
    
    def test_modules_exist(self):
        """Check all modules exist"""
        modules = [
            "backend/api",
            "backend/boinc",
            "backend/gdc",
            "backend/neo4j",
            "backend/pipeline"
        ]
        
        for module in modules:
            assert Path(module).exists()
            assert Path(f"{module}/__init__.py").exists()
    
    def test_frontend_exists(self):
        """Check frontend files"""
        assert Path("frontend").exists()
        assert Path("frontend/index.html").exists()
    
    def test_documentation_exists(self):
        """Check documentation files"""
        docs = [
            "README.md",
            "QUICKSTART.md",
            "USER_GUIDE.md",
            "GRAPHQL_EXAMPLES.md",
            "PROJECT_SUMMARY.md"
        ]
        
        for doc in docs:
            assert Path(doc).exists()


class TestSetupScripts:
    """Test setup scripts"""
    
    def test_setup_scripts_exist(self):
        """Check setup scripts"""
        assert Path("setup.ps1").exists()
        assert Path("setup.sh").exists()
    
    def test_run_script_exists(self):
        """Check run script"""
        assert Path("run.py").exists()
    
    def test_docker_compose_exists(self):
        """Check Docker compose file"""
        assert Path("docker-compose.yml").exists()


if __name__ == "__main__":
    pytest.main([__file__, "-v"])