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_json(mkdir, dictwriter, ju_read_url_get, ju_read,
ju_write, from_csv, mock_read_json):
@cacheable()
def get_hemispheres():
return RmaApi().model_query(model='Hemisphere')
with patch(builtins.__name__ + '.open',
mock_open(),
create=True) as open_mock:
open_mock.return_value.write = MagicMock()
df = get_hemispheres(path='/xyz/example.csv',
strategy='create',
**Cache.cache_csv_json())
assert 'whatever' in df[0]
ju_read_url_get.assert_called_once_with(
'http://api.brain-map.org/api/v2/data/query.json?q=model::Hemisphere')
from_csv.assert_called_once_with('/xyz/example.csv')
dictwriter.return_value.writerow.assert_called()
assert not mock_read_json.called, 'pj.read_json should not have been called'
assert not ju_write.called, 'ju.write should not have been called'
assert not ju_read.called, 'json read should not have been called'
mkdir.assert_called_once_with('/xyz')
open_mock.assert_called_once_with('/xyz/example.csv', 'w')
def test_cacheable_csv_json(mkdir, dictwriter, ju_read_url_get, ju_read,
ju_write, read_csv, mock_read_json):
@cacheable()
def get_hemispheres():
return RmaApi().model_query(model='Hemisphere')
with patch(builtins.__name__ + '.open',
mock_open(),
create=True) as open_mock:
open_mock.return_value.write = MagicMock()
df = get_hemispheres(path='/xyz/example.csv',
strategy='create',
**Cache.cache_csv_json())
assert 'whatever' in df[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/example.csv', parse_dates=True)
dictwriter.return_value.writerow.assert_called()
assert not mock_read_json.called, 'pj.read_json should not have been called'
assert not ju_write.called, 'ju.write should not have been called'
assert not ju_read.called, 'json read should not have been called'
mkdir.assert_called_once_with('/xyz')
open_mock.assert_called_once_with('/xyz/example.csv', 'w')
