def download_model_nwb_if_model_exists_in_SDD(ends_with, specimen_id_directory,
s):
'''
Downloads the .nwb file and returns it's path for the specified model if the
corresponding model exists in the structured data directory
inputs:
ends_with: string that is to be matched with a file in the structured data directory in
order to return a value. i.e. if GLIF2 is being requested but there is not GLIF2 file in the
structured data directory, a nan will be returned regardless of whether there is a value of explain
variance in the database. For example this would happen if the model was excluded from
analysis because of an aberrant parameter.
specimen_id_directory: path to the structured data directory used in the rest of analysis
s: search string in the neuronal model name
returns:
either a nan or the path of the Allen Institute model .nwb file.
'''
sp_id = os.path.basename(specimen_id_directory)[:9]
if sp_id == '580895033':
print 'skipping 580895033 which is not in the api, returning np.nan'
return np.nan
if len(glif_api.get_neuronal_models(
int(sp_id))) > 1: #basic check that data is the form expected
raise Exception('why is there more than one list for %d' % sp_id)
# get models for the neuron
nms = glif_api.get_neuronal_models(int(sp_id))[0]['neuronal_models']
wkf_ids = [[
m['name'], m['neuronal_model_runs'][0]['well_known_files'][0]['id']
] for m in nms] #list
if np.any(
[f.endswith(ends_with) for f in os.listdir(specimen_id_directory)]):
LIF_binary = [s in p[0] for p in wkf_ids]
if np.any(LIF_binary):
base_path = os.path.join(os.path.dirname(os.getcwd()),
'model_nwb_files')
download_path = os.path.join(
base_path, sp_id + '_' + ends_with[1:7] + 'model.nwb')
# if the file does not already exist locally, download it
try:
os.stat(base_path)
except:
os.mkdir(base_path)
if not os.path.isfile(download_path):
wkf_id = wkf_ids[np.where(LIF_binary)[0][0]][1]
url = Api().construct_well_known_file_download_url(wkf_id)
Api().retrieve_file_over_http(url, download_path)
return download_path
else:
raise Exception('there is %s in the directory but not in the api' %
s)
else:
return np.nan
def api():
ju.read_url_post = \
MagicMock(name='read_url_post',
return_value={ 'whatever': True })
api = Api()
return api
def timeout_download_api():
error_timeout = socket.timeout
urllib_request.urlopen = Mock(side_effect=error_timeout)
api = Api()
api._log.error = Mock()
# api.retrieve_file_over_http = MagicMock()
return api
class ApiTests(unittest.TestCase):
def __init__(self, *args, **kwargs):
super(ApiTests, self).__init__(*args, **kwargs)
def setUp(self):
self.api = Api()
def tearDown(self):
self.api = None
def test_do_query_post(self):
ju.read_url_post = MagicMock(name="read_url_post", return_value={"whatever": True})
self.api.do_query(lambda *a, **k: "http://localhost/%s" % (a[0]), lambda d: d, "wow", post=True)
ju.read_url_post.assert_called_once_with("http://localhost/wow")
def test_do_query_get(self):
ju.read_url_get = MagicMock(name="read_url_get", return_value={"whatever": True})
self.api.do_query(lambda *a, **k: "http://localhost/%s" % (a[0]), lambda d: d, "wow", post=False)
ju.read_url_get.assert_called_once_with("http://localhost/wow")
def test_load_api_schema(self):
ju.read_url_get = MagicMock(name="read_url_get", return_value={"whatever": True})
self.api.load_api_schema()
ju.read_url_get.assert_called_once_with("http://api.brain-map.org/api/v2/data/enumerate.json")
def failed_download_api():
error404 = urllib_error.HTTPError(code=404,
msg='not found',
hdrs=Mock(),
fp=Mock(),
url='')
urllib_request.urlopen = Mock(side_effect=error404)
api = Api()
api._log.error = Mock()
# api.retrieve_file_over_http = MagicMock()
return api
def api():
return Api()
def setUp(self):
self.api = Api()
