def __init__(self,
one=None,
globus_client_id=None,
local_endpoint=None,
label='ibllib patch'):
assert globus_client_id
assert one
self.local_endpoint = local_endpoint or globus.get_local_endpoint()
self.label = label
self.transfer_client = globus.login_auto(
globus_client_id=globus_client_id, str_app='globus/admin')
# transfers/delete from the current computer to the flatiron: mandatory and executed first
self.globus_transfer = globus_sdk.TransferData(self.transfer_client,
self.local_endpoint,
FLAT_IRON_GLOBUS_ID,
verify_checksum=True,
sync_level='checksum',
label=label)
self.globus_delete = globus_sdk.DeleteData(self.transfer_client,
FLAT_IRON_GLOBUS_ID,
verify_checksum=True,
sync_level='checksum',
label=label)
# get a dictionary of data repositories from Alyx (with globus ids)
self.repos = {
r['name']: r
for r in one.alyx.rest('data-repository', 'list')
}
# transfers/delete from flatiron to optional third parties to synchronize / delete
self.globus_transfers_locals = {}
self.globus_deletes_locals = {}
super().__init__(one=one)
def test_login_auto(self, mock_params):
client_id = 'h3u2i'
# Test ValueError thrown with incorrect parameters
mock_params.return_value = None # No parameters saved
with self.assertRaises(ValueError):
globus.login_auto(client_id)
mock_params.assert_called_with('globus/default')
pars = params.from_dict({'access_token': '7r3hj89', 'expires_at_seconds': '2020-09-10'})
mock_params.return_value = pars # Incomplete parameter object
with self.assertRaises(ValueError):
globus.login_auto(client_id)
# Complete parameter object
mock_params.return_value = pars.set('refresh_token', '37yh4')
gtc = globus.login_auto(client_id)
self.assertIsInstance(gtc, unittest.mock.Mock)
mock, _ = self.patcher.get_original()
mock.assert_called_once_with(client_id)
LOCAL_REPO = p.local_endpoint # Endpoint UUID from Website
SERVER_ID = p.remote_endpoint # FlatIron
DST_DIR = params.read('ibl_ci', {'data_root': '.'}).data_root
GLOBUS_CLIENT_ID = oneibl.params.get().GLOBUS_CLIENT_ID
# Constants
SRC_DIR = '/integration'
POLL = (5, 60*60) # min max seconds between pinging server
TIMEOUT = 24*60*60 # seconds before timeout
status_map = {
'ACTIVE': ('QUEUED', 'ACTIVE'),
'FAILED': ('ENDPOINT_ERROR', 'PERMISSION_DENIED', 'CONNECT_FAILED'),
'INACTIVE': 'PAUSED_BY_ADMIN'
}
try:
gtc = globus.login_auto(GLOBUS_CLIENT_ID, str_app='globus/admin')
except ValueError:
logger.info('User authentication required...')
globus.setup(GLOBUS_CLIENT_ID)
gtc = globus.login_auto(GLOBUS_CLIENT_ID)
# Check path exists
try:
gtc.operation_ls(SERVER_ID, path=SRC_DIR)
except TransferAPIError as ex:
logger.error(f'Failed to query source endpoint path {SRC_DIR}')
raise ex
# Create the destination path if it does not exist
dst_directory = as_globus_path(DST_DIR)
LOCAL_REPO = p.local_endpoint # Endpoint UUID from Website
SERVER_ID = p.remote_endpoint # FlatIron
GLOBUS_CLIENT_ID = p.GLOBUS_CLIENT_ID
DST_DIR = params.read('ibl_ci', {'data_root': '.'}).data_root
# Constants
SRC_DIR = '/integration'
POLL = (5, 60 * 60) # min max seconds between pinging server
TIMEOUT = 24 * 60 * 60 # seconds before timeout
status_map = {
'ACTIVE': ('QUEUED', 'ACTIVE'),
'FAILED': ('ENDPOINT_ERROR', 'PERMISSION_DENIED', 'CONNECT_FAILED'),
'INACTIVE': 'PAUSED_BY_ADMIN'
}
try:
gtc = globus.login_auto(GLOBUS_CLIENT_ID)
except ValueError:
logger.info('User authentication required...')
globus.setup(GLOBUS_CLIENT_ID)
gtc = globus.login_auto(GLOBUS_CLIENT_ID)
# Check path exists
try:
gtc.operation_ls(SERVER_ID, path=SRC_DIR)
except TransferAPIError as ex:
logger.error(f'Failed to query source endpoint path {SRC_DIR}')
raise ex
# Create the destination path if it does not exist
dst_directory = as_globus_path(DST_DIR)
def __init__(self, **kwargs):
# Init connection to the database
super(OneGlobus, self).__init__(**kwargs)
# Init connection to Globus if needed
self._tc = globus.login_auto(par.GLOBUS['CLIENT_ID'], str_app='globus_one')
def setup(self):
super(OneGlobus, self).setup()
globus.login_auto(par.GLOBUS['CLIENT_ID'], str_app='globus_one')