Merge pull request #738 from int-brain-lab/alignment_uploads

Alignment uploads

Author: mayofaulkner

ibllib/oneibl/patcher.py

@@ -101,7 +101,7 @@ def __init__(self, one=None):
         assert one
         self.one = one
 
-    def _patch_dataset(self, path, dset_id=None, dry=False, ftp=False):
+    def _patch_dataset(self, path, dset_id=None, revision=None, dry=False, ftp=False):
         """
         This private methods gets the dataset information from alyx, computes the local
         and remote paths and initiates the file copy
@@ -113,6 +113,10 @@ def _patch_dataset(self, path, dset_id=None, dry=False, ftp=False):
                 dset_id = None
         assert dset_id
         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:
+            path = path.parent.joinpath(f'#{revision}#', path.name)
         assert path.exists()
         dset = self.one.alyx.rest('datasets', 'read', id=dset_id)
         fr = next(fr for fr in dset['file_records'] if 'flatiron' in fr['data_repository'])
@@ -185,7 +189,7 @@ def patch_dataset(self, file_list, dry=False, ftp=False, **kwargs):
             return
         # from the dataset info, set flatIron flag to exists=True
         for p, d in zip(file_list, response):
-            self._patch_dataset(p, dset_id=d['id'], dry=dry, ftp=ftp)
+            self._patch_dataset(p, dset_id=d['id'], revision=d['revision'], dry=dry, ftp=ftp)
         return response
 
     def patch_datasets(self, file_list, **kwargs):

ibllib/qc/alignment_qc.py

@@ -2,6 +2,7 @@
 
 import numpy as np
 from pathlib import Path
+from datetime import date
 
 from neuropixel import trace_header
 import spikeglx
@@ -166,7 +167,7 @@ def run(self, update=True, upload_alyx=True, upload_flatiron=True):
 
         return results
 
-    def resolve_manual(self, align_key, update=True, upload_alyx=True, upload_flatiron=True,
+    def resolve_manual(self, align_key, update=True, upload_alyx=True, upload_flatiron=False,
                        force=False):
         """
         Method to manually resolve the alignment of a probe insertion with a given alignment
@@ -193,6 +194,7 @@ def resolve_manual(self, align_key, update=True, upload_alyx=True, upload_flatir
             results['alignment_resolved'] = True
             results['alignment_stored'] = align_key
             results['alignment_resolved_by'] = 'experimenter'
+            results['alignment_resolved_date'] = date.today().isoformat()
 
             if update:
                 self.update_extended_qc(results)

ibllib/tests/qc/test_alignment_qc.py

@@ -7,6 +7,7 @@
 import copy
 import random
 import string
+from datetime import date
 
 from one.api import ONE
 from neuropixel import trace_header
@@ -322,7 +323,8 @@ def _02_manual_resolution_latest(self):
                 alignment_stored='2020-09-28T15:57:25_mayo',
                 alignment_count=3,
                 trajectory_created=False,
-                alignment_qc=0.604081)
+                alignment_qc=0.604081,
+                alignment_date=date.today().isoformat())
 
     def _03_manual_resolution_not_latest(self):
         align_qc = AlignmentQC(self.probe_id, one=one, brain_atlas=brain_atlas, channels=False)
@@ -338,7 +340,8 @@ def _03_manual_resolution_not_latest(self):
                 alignment_stored='2020-09-28T10:03:06_alejandro',
                 alignment_count=3,
                 trajectory_created=True,
-                alignment_qc=0.604081)
+                alignment_qc=0.604081,
+                alignment_date=date.today().isoformat())
 
     @classmethod
     def tearDownClass(cls) -> None:
@@ -347,7 +350,7 @@ def tearDownClass(cls) -> None:
 
 
 def _verify(tc, alignment_resolved=None, alignment_count=None,
-            alignment_stored=None, trajectory_created=False, alignment_qc=None):
+            alignment_stored=None, trajectory_created=False, alignment_qc=None, alignment_date=None):
     """
     For a given test case with a `probe_id` attribute, check that Alyx returns insertion records
     that match the provided parameters.
@@ -382,6 +385,8 @@ def _verify(tc, alignment_resolved=None, alignment_count=None,
                             f'&probe_id={tc.probe_id}'
                             '&provenance=Ephys aligned histology track', clobber=True)
         tc.assertNotEqual(tc.prev_traj_id == traj[0]['id'], trajectory_created)
+    if alignment_date:
+        tc.assertEqual(insertion['json']['extended_qc']['alignment_resolved_date'], alignment_date)
 
 
 class TestUploadToFlatIron(unittest.TestCase):