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Shared fixtures for Bio Nexus backend smoke tests.
Mocks heavy/unavailable dependencies (supabase, litellm, Bio, sentry, etc.)
at sys.modules level so routers can import cleanly in a local test env.
"""
import base64
import json
import os
import sys
from unittest.mock import MagicMock
import pytest
from fastapi import FastAPI
from fastapi.testclient import TestClient
# Ensure the backend app package is importable
sys.path.insert(0, os.path.join(os.path.dirname(__file__), ".."))
# ---------------------------------------------------------------------------
# Mock out heavy dependencies that aren't installed in the test env
# ---------------------------------------------------------------------------
_MOCK_MODULES = [
"supabase",
"supabase._sync.client",
"litellm",
"reportlab",
"reportlab.lib",
"reportlab.lib.pagesizes",
"reportlab.lib.styles",
"reportlab.lib.units",
"reportlab.lib.colors",
"reportlab.pdfgen",
"reportlab.pdfgen.canvas",
"reportlab.platypus",
"sentry_sdk",
"redis",
]
for mod_name in _MOCK_MODULES:
if mod_name not in sys.modules:
sys.modules[mod_name] = MagicMock()
# ---------------------------------------------------------------------------
# Minimal JWT helper
# ---------------------------------------------------------------------------
def _make_test_jwt(user_id: str = "test-user-000") -> str:
header = base64.urlsafe_b64encode(json.dumps({"alg": "none", "typ": "JWT"}).encode()).rstrip(b"=").decode()
payload = base64.urlsafe_b64encode(json.dumps({"sub": user_id}).encode()).rstrip(b"=").decode()
return f"{header}.{payload}.sig"
TEST_JWT = _make_test_jwt()
# ---------------------------------------------------------------------------
# Lightweight test app — only imports the routers we actually test
# ---------------------------------------------------------------------------
@pytest.fixture(scope="session")
def client():
"""Build a minimal FastAPI app with only the 4 routers under test."""
app = FastAPI(title="Bio Nexus Smoke Tests")
from app.routers import admet, md, function_predict, docking
app.include_router(admet.router)
app.include_router(md.router)
app.include_router(function_predict.router)
app.include_router(docking.router)
with TestClient(app, raise_server_exceptions=False) as c:
yield c
@pytest.fixture()
def auth_headers():
"""Headers dict with a valid Bearer token."""
return {"Authorization": f"Bearer {TEST_JWT}"}
# ---------------------------------------------------------------------------
# Pre-load OpenMM native libs BEFORE rdkit. OpenMM and RDKit wheels bundle
# conflicting copies of MSVC runtime DLLs (msvcp140/concrt140); importing
# rdkit first makes OpenMM's Context creation crash with an access violation.
# Loading openmm.app first resolves the conflict.
# ---------------------------------------------------------------------------
try:
import openmm.app # noqa: F401
except Exception:
pass
# ---------------------------------------------------------------------------
# Detect rdkit availability (only on HF Spaces Docker, not local dev)
# find_spec avoids actually importing rdkit, which would trigger the
# OpenMM/RDKit runtime conflict above for real-OpenMM tests.
# ---------------------------------------------------------------------------
try:
import importlib.util
HAS_RDKIT = importlib.util.find_spec("rdkit.Chem") is not None
except (ImportError, ValueError):
HAS_RDKIT = False
requires_rdkit = pytest.mark.skipif(not HAS_RDKIT, reason="rdkit not installed locally — run on HF Spaces")
# ---------------------------------------------------------------------------
# Sample molecules
# ---------------------------------------------------------------------------
SAMPLE_MOLECULES = {
"aspirin": "CC(=O)OC1=CC=CC=C1C(=O)O",
"caffeine": "CN1C=NC2=C1C(=O)N(C(=O)N2C)C",
"ibuprofen": "CC(C)CC1=CC=C(C=C1)C(C)C(=O)O",
"paracetamol": "CC(=O)NC1=CC=C(C=C1)O",
"metformin": "CN(C)C(=N)NC(=O)N",
"paclitaxel": "CC(=O)OC1C(O)CC2OC3C(O)C(=CC(=O)O3)CC(O)C12C4=CC=CC=C4C(=O)OC5C(O)C(COC(=O)C)OC(O)C5NC(=O)C6=CC=CC=C6",
"short_pseudo": "C",
}
@pytest.fixture(params=list(SAMPLE_MOLECULES.keys()), ids=list(SAMPLE_MOLECULES.keys()))
def sample_smiles(request):
name = request.param
return name, SAMPLE_MOLECULES[name]
@pytest.fixture
def valid_smiles():
return "CC(=O)OC1=CC=CC=C1C(=O)O"
@pytest.fixture
def invalid_smiles():
return "NOT_A_SMILES_12345"
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