def __init__(
self,
token=None,
nexus_endpoint="https://nexus.humanbrainproject.org/v0",
kg_query_endpoint="https://kg.humanbrainproject.eu/query",
release_endpoint="https://kg.humanbrainproject.eu/api/releases",
idm_endpoint="https://services.humanbrainproject.eu/idm/v1/api"):
if token is None:
if oauth_token_handler:
token = oauth_token_handler.get_token()
else:
try:
token = os.environ["HBP_AUTH_TOKEN"]
except KeyError:
raise AuthenticationError("No token provided.")
ep = urlparse(nexus_endpoint)
self.nexus_endpoint = nexus_endpoint
auth_client = AccessTokenClient(token)
self._nexus_client = NexusClient(scheme=ep.scheme,
host=ep.netloc,
prefix=ep.path[1:],
alternative_namespace=nexus_endpoint,
auth_client=auth_client)
self._kg_query_client = HttpClient(kg_query_endpoint,
"",
auth_client=auth_client)
self._release_client = HttpClient(release_endpoint,
"",
auth_client=auth_client,
raw=True)
self._idm_client = HttpClient(idm_endpoint,
"",
auth_client=auth_client)
self._instance_repo = self._nexus_client.instances
self.cache = {} # todo: use combined uri and rev as cache keys
def __init__(self, username=None,
password=None,
job_service="https://nmpi.hbpneuromorphic.eu/api/v2/",
quotas_service="https://quotas.hbpneuromorphic.eu",
token=None,
verify=True):
if password is None and token is None:
if have_collab_token_handler:
# if are we running in a Jupyter notebook within the Collaboratory
# the token is already available
token = oauth_token_handler.get_token()
elif os.path.exists(TOKENFILE): # check for a stored token
with open(TOKENFILE) as fp:
token = json.load(fp).get(username, None)["access_token"]
else:
# prompt for password
password = getpass.getpass()
self.username = username
self.cert = None
self.verify = verify
self.token = token
self.sleep_interval = 2.0
(scheme, netloc, path, params, query, fragment) = urlparse(job_service)
self.job_server = "%s://%s" % (scheme, netloc)
self.quotas_server = quotas_service
self.storage_client = None
self.collab_source_folder = "source_code" # remote folder into which code may be uploaded
# if a token has been given, no need to authenticate
if not self.token:
self._hbp_auth(username, password)
self.auth = HBPAuth(self.token)
try:
self._get_user_info()
except Exception as err:
if "invalid_token" in str(err):
password = getpass.getpass()
self._hbp_auth(username, password)
self.auth = HBPAuth(self.token)
self._get_user_info()
else:
raise
with open(TOKENFILE, "w") as fp:
json.dump({username: {"access_token": self.token}}, fp)
# get schema
req = requests.get(job_service, cert=self.cert, verify=self.verify, auth=self.auth)
if req.ok:
self._schema = req.json()
self.resource_map = {name: entry["list_endpoint"]
for name, entry in req.json().items()}
else:
self._handle_error(req)
def __init__(self,
username=None,
password=None,
job_service="https://nmpi.hbpneuromorphic.eu/api/v2/",
quotas_service="https://quotas.hbpneuromorphic.eu",
token=None,
verify=True):
if password is None and token is None:
if have_collab_token_handler:
# if are we running in a Jupyter notebook within the Collaboratory
# the token is already available
token = oauth_token_handler.get_token()
else:
# prompt for password
password = getpass.getpass()
self.username = username
self.cert = None
self.verify = verify
self.token = token
(scheme, netloc, path, params, query, fragment) = urlparse(job_service)
self.job_server = "%s://%s" % (scheme, netloc)
self.quotas_server = quotas_service
# if a token has been given, no need to authenticate
if not self.token:
self._hbp_auth(username, password)
self.auth = HBPAuth(self.token)
self._get_user_info()
# get schema
req = requests.get(job_service,
cert=self.cert,
verify=self.verify,
auth=self.auth)
if req.ok:
self._schema = req.json()
self.resource_map = {
name: entry["list_endpoint"]
for name, entry in req.json().items()
}
else:
self._handle_error(req)
import os
from fairgraph.client import KGClient
from fairgraph.base import as_list
from fairgraph.brainsimulation import ModelProject
import numpy as np
try:
from jupyter_collab_storage import oauth_token_handler
token = oauth_token_handler.get_token()
except ModuleNotFoundError:
try:
token = os.environ["HBP_token"]
except KeyError:
print(
'Not able to load the HBP token (neither through the jupyter_collab_storage module nor locally)'
)
def check_if_alias_is_already_taken(name):
print('comparing with KG database [...]')
client = KGClient(token,
nexus_endpoint="https://nexus.humanbrainproject.org/v0")
MODELS = ModelProject.list(client, size=10000)
NAMES = [project.name for project in MODELS]
if name in NAMES:
i0 = int(np.argwhere(np.array(NAMES, dtype=str) == name))
if type(MODELS[i0].authors) is list:
author_list = ''
for nn in list(MODELS[i0].authors):
author_list += nn.resolve(client).full_name + '; '