def get_morphology_features(self, dataframe=False, file_name=None):
"""
Download morphology features for all cells with reconstructions in the database.
Parameters
----------
file_name: string
File name to save/read the ephys features metadata as CSV.
If file_name is None, the file_name will be pulled out of the
manifest. If caching is disabled, no file will be saved.
Default is None.
dataframe: boolean
Return the output as a Pandas DataFrame. If False, return
a list of dictionaries.
"""
file_name = self.get_cache_path(
file_name, self.MORPHOLOGY_FEATURES_KEY)
if self.cache:
if dataframe:
warnings.warn("dataframe argument is deprecated.")
args = Cache.cache_csv_dataframe()
else:
args = Cache.cache_csv_json()
else:
args = Cache.nocache_json()
args['strategy'] = 'lazy'
args['path'] = file_name
return self.api.get_morphology_features(**args)
def get_morphology_features(self, dataframe=False, file_name=None):
"""
Download morphology features for all cells with reconstructions in the database.
Parameters
----------
file_name: string
File name to save/read the ephys features metadata as CSV.
If file_name is None, the file_name will be pulled out of the
manifest. If caching is disabled, no file will be saved.
Default is None.
dataframe: boolean
Return the output as a Pandas DataFrame. If False, return
a list of dictionaries.
"""
file_name = self.get_cache_path(file_name,
self.MORPHOLOGY_FEATURES_KEY)
if self.cache:
if dataframe:
warnings.warn("dataframe argument is deprecated.")
args = Cache.cache_csv_dataframe()
else:
args = Cache.cache_csv_json()
else:
args = Cache.nocache_json()
args['strategy'] = 'lazy'
args['path'] = file_name
return self.api.get_morphology_features(**args)
def test_cacheable_csv_dataframe(from_csv, dictwriter, mock_json_utilities,
mock_dataframe):
@cacheable()
def get_hemispheres():
return RmaApi().model_query(model='Hemisphere')
with patch('allensdk.config.manifest.Manifest.safe_mkdir') as mkdir:
with patch(builtins.__name__ + '.open', mock_open(),
create=True) as open_mock:
open_mock.return_value.write = MagicMock()
df = get_hemispheres(path='/xyz/abc/example.txt',
strategy='create',
**Cache.cache_csv_dataframe())
assert df.loc[:, 'whatever'][0]
mock_json_utilities.read_url_get.assert_called_once_with(
'http://api.brain-map.org/api/v2/data/query.json?q=model::Hemisphere')
mock_dataframe.from_csv.assert_called_once_with('/xyz/abc/example.txt')
assert not mock_json_utilities.write.called, 'write should not have been called'
assert not mock_json_utilities.read.called, 'read should not have been called'
mkdir.assert_called_once_with('/xyz/abc')
open_mock.assert_called_once_with('/xyz/abc/example.txt', 'w')
def test_cacheable_csv_dataframe(read_csv, dictwriter, ju_read_url_get,
ju_read, ju_write):
@cacheable()
def get_hemispheres():
return RmaApi().model_query(model='Hemisphere')
with patch('allensdk.config.manifest.Manifest.safe_mkdir') as mkdir:
with patch(builtins.__name__ + '.open',
mock_open(),
create=True) as open_mock:
open_mock.return_value.write = MagicMock()
df = get_hemispheres(path='/xyz/abc/example.txt',
strategy='create',
**Cache.cache_csv_dataframe())
assert df.loc[:, 'whatever'][0]
ju_read_url_get.assert_called_once_with(
'http://api.brain-map.org/api/v2/data/query.json?q=model::Hemisphere')
read_csv.assert_called_once_with('/xyz/abc/example.txt', parse_dates=True)
assert not ju_write.called, 'write should not have been called'
assert not ju_read.called, 'read should not have been called'
mkdir.assert_called_once_with('/xyz/abc')
open_mock.assert_called_once_with('/xyz/abc/example.txt', 'w')
