Ensure paths are str in GlobusPatcher; ignore tmin, tmax if no trials…

… start pulses detected

ibllib/io/extractors/ephys_fpga.py

@@ -832,9 +832,12 @@ def _extract(self, sync=None, chmap=None, sync_collection='raw_ephys_data',
             # in ephysChoiceWorld that tend to ruin the final trial extraction).
             t_trial_start, *_ = _assign_events_bpod(bpod['times'], bpod['polarities'])
             bpod_start = self.bpod_trials['intervals_bpod'][:, 0]
-            fcn, *_ = neurodsp.utils.sync_timestamps(bpod_start, t_trial_start)
-            tmin = fcn(trials_table['intervals'][0, 0]) - 1
-            tmax = fcn(trials_table['intervals'][-1, 1]) + 1
+            if len(t_trial_start) > len(bpod_start) / 2:
+                fcn, *_ = neurodsp.utils.sync_timestamps(bpod_start, t_trial_start)
+                tmin = fcn(trials_table['intervals'][0, 0]) - 1
+                tmax = fcn(trials_table['intervals'][-1, 1]) + 1
+            else:  # This type of alignment fails for some sessions, e.g. mesoscope
+                tmin = tmax = None
 
         # Store the cleaned frame2ttl, audio, and bpod pulses as this will be used for QC
         fpga_trials, self.frame2ttl, self.audio, self.bpod = extract_behaviour_sync(

ibllib/oneibl/patcher.py

@@ -250,6 +250,7 @@ def _scp(self, local_path, remote_path, dry=True):
             remote_path.relative_to(PurePosixPath(FLATIRON_MOUNT))
         )
         _logger.info(f"Globus copy {local_path} to {remote_path}")
+        local_path = globus.as_globus_path(local_path)
         if not dry:
             if isinstance(self.globus_transfer, globus_sdk.TransferData):
                 self.globus_transfer.add_item(local_path, remote_path.as_posix())
@@ -263,9 +264,9 @@ def _rm(self, flatiron_path, dry=True):
         _logger.info(f'Globus del {flatiron_path}')
         if not dry:
             if isinstance(self.globus_delete, globus_sdk.DeleteData):
-                self.globus_delete.add_item(flatiron_path)
+                self.globus_delete.add_item(flatiron_path.as_posix())
             else:
-                self.globus_delete.path.append(flatiron_path)
+                self.globus_delete.path.append(flatiron_path.as_posix())
         return 0, ''
 
     def patch_datasets(self, file_list, **kwargs):

ibllib/tests/qc/test_critical_reasons.py

@@ -18,7 +18,7 @@
 
 def mock_input(prompt):
     if "Select from this list the reason(s)" in prompt:
-        return "1,3"
+        return "1," + prompt[prompt.index(') Other') - 1]  # always choose last option, 'Other'
     elif "Explain why you selected" in prompt:
         return "estoy un poco preocupada"
     elif "You are about to delete" in prompt: