def test_get_age(ophys_lims_experiment_id, compare_val):
ophys_lims_api = OphysLimsApi(ophys_lims_experiment_id)
if compare_val is None:
expected_fail = False
try:
ophys_lims_api.get_age()
except OneResultExpectedError:
expected_fail = True
assert expected_fail is True
else:
assert ophys_lims_api.get_age() == compare_val
def validate_ophys_dff_length(ophys_experiment_id, api=None):
api = OphysLimsApi() if api is None else api
ophys_experiment_dir = api.get_ophys_experiment_dir(ophys_experiment_id)
raw_filepath = os.path.join(ophys_experiment_dir,
str(ophys_experiment_id) + '.h5')
raw_data_shape = get_raw_ophys_file_shape(raw_filepath)
dff_filepath = api.get_dff_file(ophys_experiment_id=ophys_experiment_id)
dff_shape = get_raw_ophys_file_shape(dff_filepath)
if raw_data_shape[0] != dff_shape[1]:
raise ValidationError('dff length does not match raw data length')
def test_get_rigid_motion_transform_file(ophys_experiment_id, api_data):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
f = ophys_lims_api.get_rigid_motion_transform_file
key = 'rigid_motion_transform_file'
if ophys_experiment_id in api_data:
assert f() == api_data[ophys_experiment_id][key]
else:
expected_fail(f)
def test_average_intensity_projection_image(ophys_experiment_id, api_data):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
f = ophys_lims_api.get_average_intensity_projection_image_file
key = 'avgint_a1X_file'
if ophys_experiment_id in api_data:
assert f() == api_data[ophys_experiment_id][key]
else:
expected_fail(f)
def test_get_maxint_file(ophys_experiment_id, api_data):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
f = ophys_lims_api.get_max_projection_file
key = 'maxint_file'
if ophys_experiment_id in api_data:
assert f() == api_data[ophys_experiment_id][key]
else:
expected_fail(f)
def test_get_ophys_experiment_dir(ophys_experiment_id, api_data):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
f = ophys_lims_api.get_ophys_experiment_dir
key = 'ophys_dir'
if ophys_experiment_id in api_data:
assert f() == os.path.normpath(api_data[ophys_experiment_id][key])
else:
expected_fail(f)
def test_get_workflow_state(ophys_experiment_id, api_data):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
f = ophys_lims_api.get_workflow_state
key = 'workflow_state'
if ophys_experiment_id in api_data:
assert f() == api_data[ophys_experiment_id][key]
else:
expected_fail(f)
def test_get_LabTracks_ID(ophys_experiment_id, api_data):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
f = ophys_lims_api.get_external_specimen_name
key = 'LabTracks_ID'
if ophys_experiment_id in api_data:
assert f() == api_data[ophys_experiment_id][key]
else:
expected_fail(f)
def test_get_full_genotype(ophys_experiment_id, api_data):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
f = ophys_lims_api.get_full_genotype
key = 'full_genotype'
if ophys_experiment_id in api_data:
assert f() == api_data[ophys_experiment_id][key]
else:
expected_fail(f)
def test_get_driver_line(ophys_experiment_id, api_data):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
f = ophys_lims_api.get_driver_line
key = 'driver_line'
if ophys_experiment_id in api_data:
assert f() == api_data[ophys_experiment_id][key]
else:
expected_fail(f)
def test_get_stimulus_name(ophys_experiment_id, api_data):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
f = ophys_lims_api.get_stimulus_name
key = 'stimulus_name'
if ophys_experiment_id in api_data:
assert f() == api_data[ophys_experiment_id][key]
else:
expected_fail(f)
def test_get_imaging_depth(ophys_experiment_id, api_data):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
f = ophys_lims_api.get_imaging_depth
key = 'imaging_depth'
if ophys_experiment_id in api_data:
assert f() == api_data[ophys_experiment_id][key]
else:
expected_fail(f)
def test_get_targeted_structure(ophys_experiment_id, api_data):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
f = ophys_lims_api.get_targeted_structure
key = 'targeted_structure'
if ophys_experiment_id in api_data:
assert f() == api_data[ophys_experiment_id][key]
else:
expected_fail(f)
def test_get_cell_roi_table(ophys_experiment_id):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
assert len(ophys_lims_api.get_cell_specimen_table()) == 128
def test_get_ophys_segmentation_run_id(ophys_experiment_id):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
_ = ophys_lims_api.get_ophys_cell_segmentation_run_id()
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
_ = ophys_lims_api.get_ophys_cell_segmentation_run_id()
@pytest.mark.requires_bamboo
@pytest.mark.parametrize('ophys_experiment_id', [
pytest.param(511458874),
])
def test_get_cell_roi_table(ophys_experiment_id):
ophys_lims_api = OphysLimsApi(ophys_experiment_id)
assert len(ophys_lims_api.get_cell_specimen_table()) == 128
@pytest.mark.requires_bamboo
@pytest.mark.parametrize('ophys_lims_api, compare_val', [
pytest.param(OphysLimsApi(511458874), 0.785203),
pytest.param(OphysLimsApi(0), None)
])
def test_get_surface_2p_pixel_size_um(ophys_lims_api, compare_val):
if compare_val is None:
expected_fail = False
try:
ophys_lims_api.get_surface_2p_pixel_size_um()
except OneResultExpectedError:
expected_fail = True
assert expected_fail is True
else:
assert ophys_lims_api.get_surface_2p_pixel_size_um() == compare_val