def bo_api_save_ophys():
bo = BrainObservatoryApi('http://testwarehouse:9000')
bo.json_msg_query = \
MagicMock(name='json_msg_query',
return_value=[{'download_link': '/url/path/to/file'}])
return bo
def __init__(self,
cache=True,
manifest_file='brain_observatory_manifest.json',
base_uri=None):
super(BrainObservatoryCache, self).__init__(manifest=manifest_file,
cache=cache)
self.api = BrainObservatoryApi(base_uri=base_uri)
def cell_specimen_table(md_temp_dir):
# download a zipped version of the cell specimen table for filter tests
# as it is orders of magnitude faster
api = BrainObservatoryApi()
zipped = os.path.join(md_temp_dir, "cell_specimens.zip")
api.retrieve_file_over_http(CELL_SPECIMEN_ZIP_URL, zipped)
df = pd.read_csv(ZipFile(zipped).open("cell_metrics.csv"),
true_values="t", false_values="f")
js = json.loads(df.to_json(orient="records"))
table_file = os.path.join(md_temp_dir, "cell_specimens.json")
with open(table_file, "w") as f:
json.dump(js, f, indent=1)
return table_file
def __init__(self,
cache=True,
manifest_file='brain_observatory_manifest.json',
base_uri=None,
api=None):
super(BrainObservatoryCache,
self).__init__(manifest=manifest_file,
cache=cache,
version=self.MANIFEST_VERSION)
if api is None:
self.api = BrainObservatoryApi(base_uri=base_uri)
else:
self.api = api
def __init__(self,
cache=True,
manifest_file=None,
base_uri=None,
api=None):
if manifest_file is None:
manifest_file = get_default_manifest_file('brain_observatory')
super(BrainObservatoryCache,
self).__init__(manifest=manifest_file,
cache=cache,
version=self.MANIFEST_VERSION)
if api is None:
self.api = BrainObservatoryApi(base_uri=base_uri)
else:
self.api = api
def bo_api():
bo = BrainObservatoryApi('http://testwarehouse:9000')
bo.json_msg_query = MagicMock(name='json_msg_query')
return bo
def api():
boi = BrainObservatoryApi()
return boi
def bo_api():
endpoint = os.environ[
'TEST_API_ENDPOINT'] if 'TEST_API_ENDPOINT' in os.environ else 'http://twarehouse-backup'
return BrainObservatoryApi(endpoint)
def make_bo_api():
from allensdk.api.queries.brain_observatory_api import BrainObservatoryApi
endpoint = os.environ['TEST_API_ENDPOINT'] if 'TEST_API_ENDPOINT' in os.environ else 'http://twarehouse-backup'
return BrainObservatoryApi(endpoint)
