CI test fixes

ibllib/pipes/misc.py

@@ -74,7 +74,7 @@ def create_alyx_probe_insertions(
     for plabel in labels:
         insdict = {"session": eid, "name": plabel, "model": pmodel, "json": qc_dict}
         # search for the corresponding insertion in Alyx
-        alyx_insertion = one.alyx.get(f'/insertions?&session={eid}&name={plabel}', clobber=True)
+        alyx_insertion = one.alyx.get(f'/insertions?&session={str(eid)}&name={plabel}', clobber=True)
         # if it doesn't exist, create it
         if len(alyx_insertion) == 0:
             alyx_insertion = one.alyx.rest("insertions", "create", data=insdict)

ibllib/plots/snapshot.py

@@ -6,6 +6,7 @@
 import numpy as np
 
 from one.api import ONE
+from one.alf.spec import is_uuid
 from ibllib.pipes import tasks
 from one.alf.exceptions import ALFObjectNotFound
 from neuropixel import trace_header, TIP_SIZE_UM
@@ -177,6 +178,8 @@ class Snapshot:
 
     def __init__(self, object_id, content_type='session', one=None):
         self.one = one or ONE()
+        if not is_uuid(object_id, versions=(4,)):
+            raise ValueError('Expected `object_id` to be a UUIDv4 object')
         self.object_id = object_id
         self.content_type = content_type
         self.images = []
@@ -217,13 +220,14 @@ def register_image(self, image_file, text='', json_field=None, width=None):
         # the protocol is not compatible with byte streaming and json, so serialize the json object here
         # Make sure that user is logged in, if not, try to log in
         assert self.one.alyx.is_logged_in, 'No Alyx user is logged in, try running one.alyx.authenticate() first'
+        object_id = str(self.object_id)  # ensure not UUID object
         note = {
-            'user': self.one.alyx.user, 'content_type': self.content_type, 'object_id': self.object_id,
+            'user': self.one.alyx.user, 'content_type': self.content_type, 'object_id': object_id,
             'text': text, 'width': width, 'json': json.dumps(json_field)}
-        _logger.info(f'Registering image to {self.content_type} with id {self.object_id}')
+        _logger.info(f'Registering image to {self.content_type} with id {object_id}')
         # to make sure an eventual note gets deleted with the image call the delete REST endpoint first
         current_note = self.one.alyx.rest('notes', 'list',
-                                          django=f"object_id,{self.object_id},text,{text},json__name,{text}",
+                                          django=f"object_id,{object_id},text,{text},json__name,{text}",
                                           no_cache=True)
         if len(current_note) == 1:
             self.one.alyx.rest('notes', 'delete', id=current_note[0]['id'])
@@ -235,7 +239,7 @@ def register_image(self, image_file, text='', json_field=None, width=None):
             return note_db
         except requests.HTTPError as e:
             if 'matching query does not exist' in str(e):
-                _logger.error(f'The object_id {self.object_id} does not match an object of type {self.content_type}')
+                _logger.error(f'The object_id {object_id} does not match an object of type {self.content_type}')
                 _logger.debug(traceback.format_exc())
             else:
                 raise e

ibllib/qc/critical_reasons.py

@@ -10,6 +10,7 @@
 import json
 from datetime import datetime
 from one.webclient import AlyxClient
+from one.alf.spec import is_uuid
 
 _logger = logging.getLogger('ibllib')
 
@@ -83,8 +84,8 @@ def main(uuid, alyx=None):
     # ask reasons for selection of critical status
 
     # hit the database to know if uuid is insertion or session uuid
-    sess_list = alyx.get('/sessions?&django=pk,' + uuid, clobber=True)
-    ins_list = alyx.get('/insertions?&django=pk,' + uuid, clobber=True)
+    sess_list = alyx.get('/sessions?&django=pk,' + str(uuid), clobber=True)
+    ins_list = alyx.get('/insertions?&django=pk,' + str(uuid), clobber=True)
 
     if len(sess_list) > 0 and len(ins_list) == 0:  # session
         note = CriticalSessionNote(uuid, alyx)
@@ -131,6 +132,8 @@ def __init__(self, uuid, alyx, content_type=None):
         content_type : str
             The Alyx model name of the UUID.
         """
+        if not is_uuid(uuid, versions=(4,)):
+            raise ValueError('Expected `uuid` to be a UUIDv4 object')
         self.uuid = uuid
         self.alyx = alyx
         self.selected_reasons = []
@@ -237,7 +240,8 @@ def _delete_notes(self, notes):
             self._delete_note(note['id'])
 
     def _check_existing_note(self):
-        notes = self.alyx.rest('notes', 'list', django=f'text__icontains,{self.note_title},object_id,{self.uuid}', no_cache=True)
+        query = f'text__icontains,{self.note_title},object_id,{str(self.uuid)}'
+        notes = self.alyx.rest('notes', 'list', django=query, no_cache=True)
         if len(notes) == 0:
             return False, None
         else:

requirements.txt

@@ -27,7 +27,7 @@ ibl-neuropixel>=1.6.2
 iblutil>=1.13.0
 iblqt>=0.4.2
 mtscomp>=1.0.1
-ONE-api==3.0b3
+ONE-api==3.0b4
 phylib>=2.6.0
 psychofit
 slidingRP>=1.1.1  # steinmetz lab refractory period metrics