def test_verify_dataset_exit_codes(dataset, exit_status_expected, monkeypatch):
# get the exit status from the script
def sys_exit(status):
return status
monkeypatch.setattr(sys, "exit", sys_exit)
h5path = retrieve_data(dataset)
exit_status = cli.verify_dataset(h5path)
assert exit_status == exit_status_expected
def test_verify_dataset_exit_code_alert(monkeypatch):
# get the exit status from the script
def sys_exit(status):
return status
monkeypatch.setattr(sys, "exit", sys_exit)
h5path = retrieve_data("fmt-hdf5_fl_2018.zip")
# provoke a warning
with h5py.File(h5path, "r+") as h5:
h5.attrs["experiment:unknown"] = ""
with mock.patch("sys.argv", ["", str(h5path)]):
exit_status = cli.verify_dataset(h5path)
assert exit_status == 1 # unknown key leads to alert
def test_verify_dataset_exit_code_violation_1(monkeypatch):
# get the exit status from the script
def sys_exit(status):
return status
monkeypatch.setattr(sys, "exit", sys_exit)
h5path = retrieve_data("fmt-hdf5_fl_2018.zip")
# Since 0.35.0 we really check the configuration key types.
# Just make sure that they are properly set:
with h5py.File(h5path, "a") as h5:
for key in ["fluorescence:sample rate",
"imaging:roi position x",
"imaging:roi position y"]:
h5.attrs[key] = int(h5.attrs[key])
# provoke a warning
with h5py.File(h5path, "r+") as h5:
h5.attrs["setup:flow rate"] = 0
exit_status = cli.verify_dataset(h5path)
assert exit_status == 3 # zero flow rate and warnings about mismatch