Merge pull request #750 from int-brain-lab/protected_view

Protected view

Author: mayofaulkner

ibllib/oneibl/patcher.py

@@ -115,7 +115,7 @@ def _patch_dataset(self, path, dset_id=None, revision=None, dry=False, ftp=False
         assert is_uuid_string(dset_id)
         # If the revision is not None then we need to add the revision into the path. Note the moving of the file
         # is handled by one registration client
-        if revision is not None:
+        if revision is not None and f'#{revision}' not in str(path):
             path = path.parent.joinpath(f'#{revision}#', path.name)
         assert path.exists()
         dset = self.one.alyx.rest('datasets', 'read', id=dset_id)

ibllib/oneibl/registration.py

@@ -12,6 +12,7 @@
 from one.converters import ConversionMixin
 import one.alf.exceptions as alferr
 from one.util import datasets2records, ensure_list
+from one.api import ONE
 
 import ibllib
 import ibllib.io.extractors.base
@@ -78,6 +79,25 @@ def register_dataset(file_list, one=None, exists=False, versions=None, **kwargs)
     assert all(Path(f).exists() for f in file_list)
 
     client = IBLRegistrationClient(one)
+
+    # Check for protected datasets
+    # Account for cases where we are connected to cortex lab database
+    if one.alyx.base_url == 'https://alyx.cortexlab.net':
+        protected_status = IBLRegistrationClient(
+            ONE(base_url='https://alyx.internationalbrainlab.org', mode='remote')).check_protected_files(file_list)
+    else:
+        protected_status = client.check_protected_files(file_list)
+
+    if isinstance(protected_status, list):
+        protected = any(d['status_code'] == 403 for d in protected_status)
+    else:
+        protected = protected_status['status_code'] == 403
+
+    # If we find a protected dataset, and we don't have a force=True flag, raise an error
+    if protected and not kwargs.pop('force', False):
+        raise FileExistsError('Protected datasets were found in the file list. To force the registration of datasets '
+                              'add the force=True argument.')
+
     # If the repository is specified then for the registration client we want server_only=True to
     # make sure we don't make any other repositories for the lab
     if kwargs.get('repository') and not kwargs.get('server_only', False):

ibllib/pipes/histology.py

@@ -237,24 +237,22 @@ def register_chronic_track(chronic_id, picks=None, one=None, overwrite=False, ch
     :return:
     """
     assert one
-    brain_locations, insertion_histology = register_track(chronic_id, picks=picks, one=one, overwrite=overwrite,
-                                                          channels=channels, brain_atlas=brain_atlas,
-                                                          endpoint='chronic-insertions')
-
-    # Update all the associated probe insertions with the relevant QC and xyz_picks
     chronic = one.alyx.rest('chronic-insertions', 'list', id=chronic_id)[0]
     for probe_id in chronic['probe_insertion']:
         pid = probe_id['id']
-        if picks is None or picks.size == 0:
-            hist_qc = base.QC(pid, one=one, endpoint='insertions')
-            hist_qc.update_extended_qc({'tracing_exists': False})
-            hist_qc.update('CRITICAL', namespace='tracing')
-        else:
-            one.alyx.json_field_update(endpoint='insertions', uuid=pid, field_name='json',
-                                       data={'xyz_picks': np.int32(picks * 1e6).tolist()})
-            # Update the insertion qc to register tracing exits
-            hist_qc = base.QC(pid, one=one, endpoint='insertions')
-            hist_qc.update_extended_qc({'tracing_exists': True})
+        brain_locations, insertion_histology = register_track(pid, picks=picks, one=one, overwrite=overwrite,
+                                                              channels=channels, brain_atlas=brain_atlas)
+
+    if picks is None or picks.size == 0:
+        hist_qc = base.QC(chronic_id, one=one, endpoint='chronic-insertions')
+        hist_qc.update_extended_qc({'tracing_exists': False})
+        hist_qc.update('CRITICAL', namespace='tracing')
+    else:
+        one.alyx.json_field_update(endpoint='chronic-insertions', uuid=chronic_id, field_name='json',
+                                   data={'xyz_picks': np.int32(picks * 1e6).tolist()})
+        # Update the insertion qc to register tracing exits
+        hist_qc = base.QC(chronic_id, one=one, endpoint='chronic-insertions')
+        hist_qc.update_extended_qc({'tracing_exists': True})
 
     return brain_locations, insertion_histology
 
@@ -291,7 +289,14 @@ def register_track(probe_id, picks=None, one=None, overwrite=False, channels=Tru
         insertion_histology = None
         # Here need to change the track qc to critical and also extended qc to zero
     else:
-        brain_locations, insertion_histology = get_brain_regions(picks, brain_atlas=brain_atlas)
+        try:
+            eid, pname = one.pid2eid(probe_id)
+            chan_pos = one.load_dataset(eid, 'channels.localCoordinates.npy', collection=f'alf/{pname}/pykilosort')
+        except Exception:
+            chan_pos = None
+
+        brain_locations, insertion_histology = get_brain_regions(picks, channels_positions=chan_pos,
+                                                                 brain_atlas=brain_atlas)
         # 1) update the alyx models, first put the picked points in the insertion json
         one.alyx.json_field_update(endpoint=endpoint, uuid=probe_id, field_name='json',
                                    data={'xyz_picks': np.int32(picks * 1e6).tolist()})
@@ -391,8 +396,10 @@ def create_trajectory_dict(probe_id, insertion, provenance, endpoint='insertions
              }
     if endpoint == 'chronic-insertions':
         tdict['chronic_insertion'] = probe_id
+        tdict['probe_insertion'] = None
     else:
         tdict['probe_insertion'] = probe_id
+        tdict['chronic_insertion'] = None
 
     return tdict
 

ibllib/plots/figures.py

@@ -785,7 +785,11 @@ def dlc_qc_plot(session_path, one=None, device_collection='raw_video_data',
     # Load session level data
     for alf_object in ['trials', 'wheel', 'licks']:
         try:
-            data[f'{alf_object}'] = alfio.load_object(session_path.joinpath(trials_collection), alf_object)  # load locally
+            if alf_object == 'licks':
+                data[f'{alf_object}'] = alfio.load_object(session_path.joinpath('alf'),
+                                                          alf_object)  # load locally
+            else:
+                data[f'{alf_object}'] = alfio.load_object(session_path.joinpath(trials_collection), alf_object)  # load locally
             continue
         except ALFObjectNotFound:
             pass

ibllib/qc/alignment_qc.py

@@ -316,7 +316,7 @@ def upload_channels(self, alignment_key, upload_alyx, upload_flatiron):
                 ephys_traj = self.one.alyx.get(f'/trajectories?&probe_insertion={self.eid}'
                                                '&provenance=Ephys aligned histology track',
                                                clobber=True)
-                patch_dict = {'json': self.alignments}
+                patch_dict = {'probe_insertion': self.eid, 'json': self.alignments}
                 self.one.alyx.rest('trajectories', 'partial_update', id=ephys_traj[0]['id'],
                                    data=patch_dict)
 

ibllib/tests/qc/test_alignment_qc.py

@@ -186,6 +186,7 @@ def _02_one_alignment(self):
                       self.alignments['2020-06-26T16:40:14_Karolina_Socha']}
         trajectory = copy.deepcopy(self.trajectory)
         trajectory.update({'json': alignments})
+        trajectory.update({'chronic_insertion': None})
         _ = one.alyx.rest('trajectories', 'create', data=trajectory)
         align_qc = AlignmentQC(self.probe_id, one=one, brain_atlas=brain_atlas, channels=False)
         align_qc.run(update=True, upload_alyx=True, upload_flatiron=False)
@@ -199,8 +200,8 @@ def _03_alignments_disagree(self):
                       self.alignments['2020-06-26T16:40:14_Karolina_Socha'],
                       '2020-06-12T00:39:15_nate': self.alignments['2020-06-12T00:39:15_nate']}
         trajectory = copy.deepcopy(self.trajectory)
-        trajectory.update({'json': alignments})
-        traj = one.alyx.rest('trajectories', 'update', id=self.prev_traj_id, data=trajectory)
+        trajectory.update({'probe_insertion': self.probe_id, 'json': alignments})
+        traj = one.alyx.rest('trajectories', 'partial_update', id=self.prev_traj_id, data=trajectory)
         align_qc = AlignmentQC(self.probe_id, one=one, brain_atlas=brain_atlas, channels=False)
         align_qc.load_data(prev_alignments=traj['json'], xyz_picks=np.array(self.xyz_picks) / 1e6,
                            cluster_chns=self.cluster_chns, depths=SITES_COORDINATES[:, 1],
@@ -216,8 +217,8 @@ def _04_alignments_agree(self):
                       self.alignments['2020-06-19T10:52:36_noam.roth'],
                       '2020-06-12T00:39:15_nate': self.alignments['2020-06-12T00:39:15_nate']}
         trajectory = copy.deepcopy(self.trajectory)
-        trajectory.update({'json': alignments})
-        traj = one.alyx.rest('trajectories', 'update', id=self.prev_traj_id, data=trajectory)
+        trajectory.update({'probe_insertion': self.probe_id, 'json': alignments})
+        traj = one.alyx.rest('trajectories', 'partial_update', id=self.prev_traj_id, data=trajectory)
         self.assertEqual(self.prev_traj_id, traj['id'])
         align_qc = AlignmentQC(self.probe_id, one=one, brain_atlas=brain_atlas, channels=False)
         align_qc.load_data(cluster_chns=self.cluster_chns, depths=SITES_COORDINATES[:, 1],
@@ -230,8 +231,8 @@ def _04_alignments_agree(self):
     def _05_not_latest_alignments_agree(self):
         alignments = copy.deepcopy(self.alignments)
         trajectory = copy.deepcopy(self.trajectory)
-        trajectory.update({'json': alignments})
-        traj = one.alyx.rest('trajectories', 'update', id=self.prev_traj_id, data=trajectory)
+        trajectory.update({'probe_insertion': self.probe_id, 'json': alignments})
+        traj = one.alyx.rest('trajectories', 'partial_update', id=self.prev_traj_id, data=trajectory)
         self.assertEqual(self.prev_traj_id, traj['id'])
         align_qc = AlignmentQC(self.probe_id, one=one, brain_atlas=brain_atlas, channels=False)
         align_qc.load_data(prev_alignments=traj['json'], xyz_picks=np.array(self.xyz_picks) / 1e6,
@@ -277,6 +278,7 @@ def setUpClass(cls) -> None:
         cls.probe_id = probe_insertion['id']
         cls.trajectory = data['trajectory'].tolist()
         cls.trajectory.update({'probe_insertion': cls.probe_id})
+        cls.trajectory.update({'chronic_insertion': None})
         cls.trajectory.update({'json': cls.alignments})
         cls.traj = one.alyx.rest('trajectories', 'create', data=cls.trajectory)
 
@@ -415,6 +417,7 @@ def setUpClass(cls) -> None:
         cls.probe_name = probe_insertion['name']
         cls.trajectory = data['trajectory'].tolist()
         cls.trajectory.update({'probe_insertion': cls.probe_id})
+        cls.trajectory.update({'chronic_insertion': None})
         cls.trajectory.update({'json': cls.alignments})
         cls.traj = one.alyx.rest('trajectories', 'create', data=cls.trajectory)
 

ibllib/tests/qc/test_task_metrics.py

@@ -17,7 +17,7 @@ class TestAggregateOutcome(unittest.TestCase):
     def test_deprecation_warning(self):
         """Remove TaskQC.compute_session_status_from_dict after 2024-04-01."""
         from datetime import datetime
-        self.assertFalse(datetime.now() > datetime(2024, 4, 1), 'remove TaskQC.compute_session_status_from_dict method.')
+        self.assertFalse(datetime.now() > datetime(2024, 4, 10), 'remove TaskQC.compute_session_status_from_dict method.')
         qc_dict = {'_task_iti_delays': .99}
         with self.assertWarns(DeprecationWarning), self.assertLogs(qcmetrics.__name__, 'WARNING'):
             out = qcmetrics.TaskQC.compute_session_status_from_dict(qc_dict)

ibllib/tests/test_oneibl.py

@@ -126,7 +126,7 @@ def test_patch_datasets(self):
 
         # Mock the post method of AlyxClient and assert that it was called during registration
         with mock.patch.object(self.one.alyx, 'post') as rest_mock:
-            rest_mock.side_effect = responses
+            rest_mock.side_effect = [[r] for r in responses]
             self.globus_patcher.patch_datasets(file_list)
             self.assertEqual(rest_mock.call_count, 2)
             for call, file in zip(rest_mock.call_args_list, file_list):
@@ -332,9 +332,14 @@ def test_registration_datasets(self):
             self.one.alyx.rest('datasets', 'partial_update',
                                id=d['url'][-36:], data={'tags': [self.tag['name']]})
 
+        # Check that we get an exception error unless force=True
+        flist = list(self.rev_path.glob('*.npy'))
+        with self.assertRaises(FileExistsError):
+            registration.register_dataset(file_list=flist, one=self.one)
+
         # Test registering with a revision already in the file path, should use this rather than create one with today's date
         flist = list(self.rev_path.glob('*.npy'))
-        r = registration.register_dataset(file_list=flist, one=self.one)
+        r = registration.register_dataset(file_list=flist, one=self.one, force=True)
         self.assertTrue(all(d['revision'] == self.revision for d in r))
         self.assertTrue(all(d['default'] for d in r))
         self.assertTrue(all(d['collection'] == 'alf' for d in r))
@@ -348,7 +353,7 @@ def test_registration_datasets(self):
         # Register again with revision in file path, it should register to self.revision + a
         flist = list(self.rev_path.glob('*.npy'))
 
-        r = registration.register_dataset(file_list=flist, one=self.one)
+        r = registration.register_dataset(file_list=flist, one=self.one, force=True)
         self.assertTrue(all(d['revision'] == f'{self.revision}a' for d in r))
         self.assertTrue(self.alf_path.joinpath(f'#{self.revision}a#', 'spikes.times.npy').exists())
         self.assertTrue(self.alf_path.joinpath(f'#{self.revision}a#', 'spikes.amps.npy').exists())
@@ -357,7 +362,7 @@ def test_registration_datasets(self):
 
         # When we re-register the original it should move them into revision with today's date
         flist = list(self.alf_path.glob('*.npy'))
-        r = registration.register_dataset(file_list=flist, one=self.one)
+        r = registration.register_dataset(file_list=flist, one=self.one, force=True)
         self.assertTrue(all(d['revision'] == self.today_revision for d in r))
         self.assertTrue(self.alf_path.joinpath(f'#{self.today_revision}#', 'spikes.times.npy').exists())
         self.assertTrue(self.alf_path.joinpath(f'#{self.today_revision}#', 'spikes.amps.npy').exists())
@@ -375,7 +380,7 @@ def test_registration_datasets(self):
         np.save(self.alf_path.joinpath('spikes.times.npy'), np.random.random(500))
         np.save(self.alf_path.joinpath('spikes.amps.npy'), np.random.random(500))
         flist = list(self.alf_path.glob('*.npy'))
-        r = registration.register_dataset(file_list=flist, one=self.one)
+        r = registration.register_dataset(file_list=flist, one=self.one, force=True)
         self.assertTrue(all(d['revision'] == self.today_revision + 'a' for d in r))
 
     def _write_settings_file(self):

requirements.txt

@@ -15,7 +15,7 @@ pynrrd>=0.4.0
 pytest
 requests>=2.22.0
 scikit-learn>=0.22.1
-scipy>=1.7.0
+scipy>=1.7.0,<1.13 # scipy gaussian missing April 2024
 scikit-image  # this is a widefield requirement missing as of July 2023, we may remove it once wfield has this figured out
 sparse
 seaborn>=0.9.0