Merge pull request #645 from int-brain-lab/restrict_cameras

PR to incorporate ONE changes

ibllib/oneibl/data_handlers.py

@@ -299,7 +299,7 @@ def uploadData(self, outputs, version, **kwargs):
 
         for collection, files in collections.items():
             globus_files = self.globus.ls(f'flatiron_{self.lab}', collection, remove_uuid=True, return_size=True)
-            file_names = [gl[0] for gl in globus_files]
+            file_names = [str(gl[0]) for gl in globus_files]
             file_sizes = [gl[1] for gl in globus_files]
 
             for name, details in files.items():

ibllib/oneibl/patcher.py

@@ -498,7 +498,7 @@ def _scp(self, local_path, remote_path, dry=True):
         _logger.info(f"Copy {local_path} to {remote_path}")
         if not dry:
             if not Path(remote_path).parent.exists():
-                Path(remote_path).parent.mkdir(exist_ok=True)
+                Path(remote_path).parent.mkdir(exist_ok=True, parents=True)
             shutil.copy(local_path, remote_path)
         return 0, ''
 

ibllib/pipes/dynamic_pipeline.py

@@ -305,8 +305,10 @@ def make_pipeline(session_path, **pkwargs):
 
     # Video tasks
     if 'cameras' in devices:
+        cams = list(devices['cameras'].keys())
+        subset_cams = [c for c in cams if c in ('left', 'right', 'body')]
         video_kwargs = {'device_collection': 'raw_video_data',
-                        'cameras': list(devices['cameras'].keys())}
+                        'cameras': cams}
         video_compressed = sess_params.get_video_compressed(acquisition_description)
 
         if video_compressed:
@@ -326,10 +328,14 @@ def make_pipeline(session_path, **pkwargs):
                 tasks[tn] = type((tn := f'VideoSyncQC_{sync}'), (vtasks.VideoSyncQcBpod,), {})(
                     **kwargs, **video_kwargs, **sync_kwargs, parents=[tasks['VideoCompress']])
             elif sync == 'nidq':
+                # Here we restrict to videos that we support (left, right or body)
+                video_kwargs['cameras'] = subset_cams
                 tasks[tn] = type((tn := f'VideoSyncQC_{sync}'), (vtasks.VideoSyncQcNidq,), {})(
                     **kwargs, **video_kwargs, **sync_kwargs, parents=[tasks['VideoCompress']] + sync_tasks)
 
         if sync_kwargs['sync'] != 'bpod':
+            # Here we restrict to videos that we support (left, right or body)
+            video_kwargs['cameras'] = subset_cams
             tasks[tn] = type((tn := 'DLC'), (vtasks.DLC,), {})(
                 **kwargs, **video_kwargs, parents=[dlc_parent_task])
             tasks['PostDLC'] = type('PostDLC', (epp.EphysPostDLC,), {})(

ibllib/pipes/video_tasks.py

@@ -270,6 +270,7 @@ def _run(self, **kwargs):
 
         mp4_files = self.session_path.joinpath(self.device_collection).glob('*.mp4')
         labels = [label_from_path(x) for x in mp4_files]
+        labels = [lab for lab in labels if lab in ('left', 'right', 'body')]
 
         kwargs = {}
         if self.sync_namespace == 'timeline':