make sure probe insertion id is not overwritten on partial update

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/pipes/histology.py

@@ -391,8 +391,10 @@ 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/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)
@@ -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)