def app_conf(request, tmpdir_factory):
dataset_path = "test-data/pbmc3k_no_raw.h5ad"
if not request.param:
app = create_app()
configure_app(app, [dataset_path], None, None)
dataset_id = dataset_path
os.environ[CIRRO_TEST] = "false"
else:
os.environ[CIRRO_TEST] = "true"
os.environ[CIRRO_DB_URI] = "mongodb://localhost:27018/cirrocumulus-test"
app = cached_app()
with app.test_client() as client:
if request.param:
# insert dataset
output_dir = str(tmpdir_factory.mktemp("data").join("test.zarr"))
PrepareData(
datasets=[anndata.read(dataset_path)],
output=output_dir,
output_format="zarr",
no_auto_groups=True,
).execute()
r = client.post("/api/dataset", data=dict(url=output_dir, name="test"))
dataset_id = r.json["id"]
yield client, dataset_id
def cached_app():
global app
if app is None:
app = create_app()
# from flask_cors import CORS
# CORS(app)
configure()
return app
def cached_app():
global app
if app is None:
app = create_app()
configure_app(app)
return app