Merge pull request #723 from int-brain-lab/hotfix/8.24.3

HOTFIX resolves #379

CHANGELOG.md

@@ -1,6 +1,10 @@
 Changelog
 =========
 
+8.24.2
+------
+* fix: create the `raw_ephys_data` folder even if there are no probes (when running behavior sessions on ephys rig)
+
 8.24.2
 ------
 * make Frame2TTL validation more robust

iblrig/__init__.py

@@ -6,7 +6,7 @@
 # 5) git tag the release in accordance to the version number below (after merge!)
 # >>> git tag 8.15.6
 # >>> git push origin --tags
-__version__ = '8.24.2'
+__version__ = '8.24.3'
 
 
 from iblrig.version_management import get_detailed_version_string

iblrig/base_tasks.py

@@ -1215,7 +1215,7 @@ def __init__(self, *_, remote_rigs=None, **kwargs):
         if isinstance(remote_rigs, list):
             # For now we flatten to list of remote rig names but could permit list of (name, URI) tuples
             remote_rigs = list(filter(None, flatten(remote_rigs)))
-            all_remote_rigs = net.get_remote_devices(iblrig_settings=kwargs.get('iblrig_settings', None))
+            all_remote_rigs = net.get_remote_devices(iblrig_settings=kwargs.get('iblrig_settings'))
             if not set(remote_rigs).issubset(all_remote_rigs.keys()):
                 raise ValueError('Selected remote rigs not in remote rigs list')
             remote_rigs = {k: v for k, v in all_remote_rigs.items() if k in remote_rigs}

iblrig/test/test_hardware_mixins.py

@@ -109,12 +109,12 @@ def test_rotary_encoder_mixin(self):
             'RotaryEncoder1_3',
             'RotaryEncoder1_4',
         ]
-        assert {
+        assert session.device_rotary_encoder.THRESHOLD_EVENTS == {
             -35: 'RotaryEncoder1_1',
             35: 'RotaryEncoder1_2',
             -2: 'RotaryEncoder1_3',
             2: 'RotaryEncoder1_4',
-        } == session.device_rotary_encoder.THRESHOLD_EVENTS
+        }
         with self.assertRaises(ValueError):
             RotaryEncoderMixin.start_mixin_rotary_encoder(session)
 

iblrig/test/test_transfers.py

@@ -6,6 +6,9 @@
 from pathlib import Path
 from unittest import mock
 
+from packaging import version
+
+import ibllib
 import iblrig.commands
 import iblrig.path_helper
 import iblrig.raw_data_loaders
@@ -228,6 +231,52 @@ def test_behavior_ephys_video_copy(self):
         self.assertEqual(set(final_experiment_description['devices']['cameras'].keys()), {'left'})
         self.assertEqual(set(final_experiment_description['sync'].keys()), {'nidq'})
 
+    # Requires recent change to ibllib test fixture code supporting no probe ephys recording files
+    @unittest.skipIf(version.parse(ibllib.__version__) < version.parse('2.39'), 'ibllib < 2.39')
+    def test_ephys_no_probe(self):
+        """Test copying a session at ephys rig when no probes were used (DAQ only)."""
+        # First create a behavior session
+        task_kwargs = copy.deepcopy(self.session_kwargs)
+        task_kwargs['hardware_settings'].update(
+            {
+                'device_cameras': None,
+                'MAIN_SYNC': False,  # this is quite important for ephys sessions
+            }
+        )
+        session = _create_behavior_session(kwargs=task_kwargs, ntrials=50)
+        folder_session_ephys = Path(self.td.name).joinpath('ephys', 'Subjects', *session.paths.SESSION_FOLDER.parts[-3:])
+
+        # Create an ephys acquisition
+        n_probes = 0
+        # SpikeGLX then saves these files into the session folder
+        populate_raw_spikeglx(folder_session_ephys, model='3B', n_probes=n_probes)
+
+        # Test the copiers
+        sc = BehaviorCopier(session_path=session.paths.SESSION_FOLDER, remote_subjects_folder=session.paths.REMOTE_SUBJECT_FOLDER)
+        self.assertEqual('.status_pending', sc.glob_file_remote_copy_status().suffix)
+        self.assertEqual(1, sc.state)
+        sc.copy_collections()
+        self.assertEqual(2, sc.state)
+        self.assertEqual('.status_complete', sc.glob_file_remote_copy_status().suffix)
+        sc.copy_collections()
+        self.assertEqual(2, sc.state)
+        sc.finalize_copy(number_of_expected_devices=None)
+        self.assertEqual(2, sc.state)  # here we still don't have all devices so we stay in state 2
+
+        ec = EphysCopier(session_path=folder_session_ephys, remote_subjects_folder=session.paths.REMOTE_SUBJECT_FOLDER)
+        self.assertEqual(0, ec.state)
+        ec.initialize_experiment()
+        self.assertEqual(1, ec.state)
+        self.assertIn('sync', ec.experiment_description)
+        ec.copy_collections()
+        self.assertEqual(2, ec.state)
+        # this time it's all there and we move on
+        ec.finalize_copy(number_of_expected_devices=None)
+        self.assertEqual(3, ec.state)
+        final_experiment_description = session_params.read_params(ec.remote_session_path)
+        self.assertEqual(1, len(final_experiment_description['tasks']))
+        self.assertEqual(set(final_experiment_description['sync'].keys()), {'nidq'})
+
     def test_copy_snapshots(self):
         """Test copy of snapshots folder(s)."""
         # Create without task data

iblrig/transfer_experiments.py

@@ -553,8 +553,9 @@ def initialize_experiment(self, acquisition_description=None, nprobes=None, main
         self._experiment_description = acquisition_description
         super().initialize_experiment(acquisition_description=acquisition_description, **kwargs)
         # once the session folders have been initialized, create the probe folders
+        (ephys_path := self.session_path.joinpath('raw_ephys_data')).mkdir(exist_ok=True)
         for n in range(nprobes):
-            self.session_path.joinpath('raw_ephys_data', f'probe{n:02}').mkdir(exist_ok=True, parents=True)
+            ephys_path.joinpath(f'probe{n:02}').mkdir(exist_ok=True)
 
     def _copy_collections(self):
         """Here we overload the copy to be able to rename the probes properly and also create the insertions."""