fix globus-sdk compatibility break

Author: oliche

ibllib/oneibl/patcher.py

@@ -243,8 +243,10 @@ def __init__(self, client_name='default', one=None, label='ibllib patch'):
         # transfers/delete from the current computer to the flatiron: mandatory and executed first
         local_id = self.endpoints['local']['id']
         self.globus_transfer = globus_sdk.TransferData(
-            self.client, local_id, flatiron_id, verify_checksum=True, sync_level='checksum', label=label)
-        self.globus_delete = globus_sdk.DeleteData(self.client, flatiron_id, label=label)
+            source_endpoint=local_id, destination_endpoint=flatiron_id,
+            verify_checksum=True, sync_level='checksum', label=label
+        )
+        self.globus_delete = globus_sdk.DeleteData(endpoint=flatiron_id, label=label)
         # transfers/delete from flatiron to optional third parties to synchronize / delete
         self.globus_transfers_locals = {}
         self.globus_deletes_locals = {}
@@ -303,7 +305,7 @@ def patch_datasets(self, file_list, **kwargs):
                 # if there is no transfer already created, initialize it
                 if repo_gid not in self.globus_transfers_locals:
                     self.globus_transfers_locals[repo_gid] = globus_sdk.TransferData(
-                        self.client, flatiron_id, repo_gid, verify_checksum=True,
+                        source_endpoint=flatiron_id, destination_endpoint=repo_gid, verify_checksum=True,
                         sync_level='checksum', label=f"{self.label} on {fr['data_repository']}")
                 # get the local server path and create the transfer item
                 local_server_path = self.to_address(fr['relative_path'], fr['data_repository'])
@@ -343,17 +345,15 @@ def _wait_for_task(resp):
             _wait_for_task(gtc.submit_transfer(self.globus_transfer))
             # re-initialize the globus_transfer property
             self.globus_transfer = globus_sdk.TransferData(
-                gtc,
-                self.globus_transfer['source_endpoint'],
-                self.globus_transfer['destination_endpoint'],
+                source_endpoint=self.globus_transfer['source_endpoint'],
+                destination_endpoint=self.globus_transfer['destination_endpoint'],
                 label=self.globus_transfer['label'],
                 verify_checksum=True, sync_level='checksum')
 
         # do the same for deletes
         if len(self.globus_delete['DATA']) > 0:
             _wait_for_task(gtc.submit_delete(self.globus_delete))
             self.globus_delete = globus_sdk.DeleteData(
-                gtc,
                 endpoint=self.globus_delete['endpoint'],
                 label=self.globus_delete['label'])
 

requirements.txt

@@ -2,7 +2,7 @@ boto3
 click>=7.0.0
 colorlog>=4.0.2
 flake8>=3.7.8
-globus-sdk
+globus-sdk>=4.0.0
 graphviz
 matplotlib>=3.0.3
 numba>=0.56
@@ -28,7 +28,7 @@ iblutil>=1.13.0
 iblqt>=0.8.2
 mtscomp>=1.0.1
 ONE-api>=3.2.0
-phylib>=2.6.0
+phylib>=2.6.2
 psychofit
 slidingRP>=1.1.1  # steinmetz lab refractory period metrics
 pyqt5