def query_mouselight(query):
"""
[Sends a GET request, not currently used for anything.]
"""
if not connected_to_internet():
raise ConnectionError(
"You need an internet connection for API queries, sorry.")
base_url = "http://ml-neuronbrowser.janelia.org/"
full_query = base_url + query
# send the query, package the return argument as a json tree
response = requests.get(full_query)
if response.ok:
json_tree = response.json()
if json_tree['success']:
return json_tree
else:
exception_string = 'did not complete api query successfully'
else:
exception_string = 'API failure. Allen says: {}'.format(
response.reason)
# raise an exception if the API request failed
raise ValueError(exception_string)
def request(url):
if not connected_to_internet():
raise ConnectionError(
"You need to have an internet connection to send requests.")
response = requests.get(url)
if response.ok:
return response
else:
exception_string = 'URL request failed: {}'.format(response.reason)
raise ValueError(exception_string)
def __init__(self, *args, **kwargs):
if not connected_to_internet():
raise ConnectionError("You will need to be connected to the internet to use the AllenMorphology class")
Paths.__init__(self, *args, **kwargs)
# Create a Cache for the Cell Types Cache API
self.ctc = CellTypesCache(manifest_file=os.path.join(self.morphology_allen, 'manifest.json'))
# Get a list of cell metadata for neurons with reconstructions, download if necessary
self.neurons = pd.DataFrame(self.ctc.get_cells(species=[CellTypesApi.MOUSE], require_reconstruction = True))
self.n_neurons = len(self.neurons)
if not self.n_neurons: raise ValueError("Something went wrong and couldn't get neurons metadata from Allen")
self.downloaded_neurons = self.get_downloaded_neurons()
def post_mouselight(url, query=None, clean=False, attempts=3):
"""
[sends a POST request to a user URL. Query can be either a string (in which case clean should be False) or a dictionary.]
"""
if not connected_to_internet():
raise ConnectionError(
"You need an internet connection for API queries, sorry.")
request = None
if query is not None:
for i in range(attempts):
try:
if not clean:
time.sleep(0.01) # avoid getting an error from server
request = requests.post(url, json={'query': query})
else:
time.sleep(0.01) # avoid getting an error from server
request = requests.post(url, json=query)
except Exception as e:
exception = e
request = None
print('MouseLight API query failed. Attempt {} of {}'.format(
i + 1, attempts))
if request is not None: break
if request is None:
raise ConnectionError(
"\n\nMouseLight API query failed with error message:\n{}.\
\nPerhaps the server is down, visit 'http://ml-neuronbrowser.janelia.org' to find out."
.format(exception))
else:
raise NotImplementedError
if request.status_code == 200:
jreq = request.json()
if 'data' in list(jreq.keys()):
return jreq['data']
else:
return jreq
else:
raise Exception(
"Query failed to run by returning code of {}. {} -- \n\n{}".format(
request.status_code, query, request.text))
def __init__(self):
SvgApi.__init__(
self
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/svg_api.py
ImageDownloadApi.__init__(
self
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/image_download_api.py
self.annsetsapi = AnnotatedSectionDataSetsApi(
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/annotated_section_data_sets_api.py
self.oapi = OntologiesApi(
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/ontologies_api.py
# Get metadata about atlases
self.atlases = pd.DataFrame(self.oapi.get_atlases_table())
self.atlases_names = sorted(list(self.atlases['name'].values))
self.mouse_coronal_atlas_id = int(self.atlases.loc[
self.atlases['name'] == "Mouse, P56, Coronal"].id.values[0])
self.mouse_sagittal_atlas_id = int(self.atlases.loc[
self.atlases['name'] == "Mouse, P56, Sagittal"].id.values[0])
self.mouse_3D_atlas_id = int(self.atlases.loc[
self.atlases['name'] == "Mouse, Adult, 3D Coronal"].id.values[0])
# Get metadata about products
if connected_to_internet():
self.products = pd.DataFrame(
send_query(
"http://api.brain-map.org/api/v2/data/query.json?criteria=model::Product"
))
self.mouse_brain_reference_product_id = 12
self.mouse_brain_ish_data_product_id = 1
self.products_names = sorted(list(self.products["name"].values))
self.mouse_products_names = sorted(
list(self.products.loc[self.products.species == "Mouse"]
["name"].values))
else:
raise ConnectionError(
"It seems that you are not connected to the internet, you won't be able to download stuff."
)