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"""
Test configuration and fixtures for GQuery AI.
This module provides common test utilities, fixtures, and configuration
for the entire test suite.
"""
import asyncio
import os
from pathlib import Path
from typing import Generator
from unittest.mock import Mock
import pytest
# Test configuration
def pytest_configure(config) -> None:
"""Configure pytest."""
# Set test environment
os.environ["ENVIRONMENT"] = "test"
os.environ["DEBUG"] = "true"
# Disable external API calls during tests
os.environ["NCBI__API_KEY"] = "test_key"
os.environ["OPENAI__API_KEY"] = "test_key"
@pytest.fixture(scope="session")
def event_loop() -> Generator[asyncio.AbstractEventLoop, None, None]:
"""Create an instance of the default event loop for the test session."""
loop = asyncio.get_event_loop_policy().new_event_loop()
yield loop
loop.close()
@pytest.fixture
def mock_settings():
"""Mock settings for testing."""
from gquery.config.settings import Settings
settings = Settings(
debug=True,
environment="test",
database=Mock(),
redis=Mock(),
ncbi=Mock(),
openai=Mock(),
logging=Mock(),
security=Mock(),
)
return settings
@pytest.fixture
def test_data_dir() -> Path:
"""Get test data directory."""
return Path(__file__).parent / "data"
@pytest.fixture
def sample_pmc_response():
"""Sample PMC API response for testing."""
return {
"esearchresult": {
"count": "2",
"retmax": "2",
"idlist": ["1234567", "7654321"]
}
}
@pytest.fixture
def sample_clinvar_response():
"""Sample ClinVar API response for testing."""
return {
"result": {
"1234": {
"title": "BRCA1, c.5266dupC (p.Gln1756ProfsTer74)",
"clinical_significance": ["Pathogenic"],
"review_status": "criteria provided, multiple submitters, no conflicts"
}
}
}
@pytest.fixture
def sample_ncbi_datasets_response():
"""Sample NCBI Datasets API response for testing."""
return {
"genes": [
{
"gene": {
"gene_id": 672,
"symbol": "BRCA1",
"description": "BRCA1, DNA repair associated",
"type": "protein-coding"
}
}
]
}
class TestCase:
"""Base test case class with common utilities."""
@staticmethod
def assert_valid_uuid(uuid_string: str) -> None:
"""Assert that a string is a valid UUID."""
from uuid import UUID
try:
UUID(uuid_string)
except ValueError:
pytest.fail(f"'{uuid_string}' is not a valid UUID")
@staticmethod
def assert_valid_timestamp(timestamp_string: str) -> None:
"""Assert that a string is a valid ISO timestamp."""
from datetime import datetime
try:
datetime.fromisoformat(timestamp_string.replace('Z', '+00:00'))
except ValueError:
pytest.fail(f"'{timestamp_string}' is not a valid ISO timestamp")
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