Merge pull request #158 from int-brain-lab/v2.11.1

v2.11.1

CHANGELOG.md

@@ -1,6 +1,12 @@
 # Changelog
-## [Latest](https://github.com/int-brain-lab/ONE/commits/main) [2.11.0]
-This version deprecates one.alf.files in preperation for replacing with one.alf.path in version 3.
+## [Latest](https://github.com/int-brain-lab/ONE/commits/main) [2.11.1]
+
+### Modified
+
+- HOTFIX: consistent behaviour in OneAlyx.list_datasets when keep_eid_index == True
+
+## [2.11.0]
+This version deprecates one.alf.files in preparation for replacing with one.alf.path in version 3.
 
 ### Modified
 
@@ -24,9 +30,9 @@ This version improves behaviour of loading revisions and loading datasets from l
 - bugfix of spurious error raised when loading dataset with a revision provided
 - default_revisions_only parameter in One.list_datasets filters non-default datasets
 - permit data frame input to One.load_datasets and load precise relative paths provided (instead of default revisions)
-- redundent session_path column has been dropped from the datasets cache table
+- redundant session_path column has been dropped from the datasets cache table
 - bugfix in one.params.setup: suggest previous cache dir if available instead of always the default
-- bugfix in one.params.setup: remove all extrenuous parameters (i.e. TOKEN) when running setup in silent mode
+- bugfix in one.params.setup: remove all extraneous parameters (i.e. TOKEN) when running setup in silent mode
 - warn user to reauthenticate when password is None in silent mode
 - always force authentication when password passed, even when token cached
 - bugfix: negative indexing of paginated response objects now functions correctly
@@ -102,7 +108,7 @@ This version of ONE adds support for Alyx 2.0.0 and pandas 3.0.0 with dataset QC
 
 - One.load_dataset
   - add an option to skip computing hash for existing files when loading datasets `check_hash=False`
-  - check filesize before computing hash for performance
+  - check file size before computing hash for performance
 
 ## [2.5.5]
 
@@ -320,7 +326,7 @@ This version of ONE adds support for Alyx 2.0.0 and pandas 3.0.0 with dataset QC
 
 - RegistrationClient.find_files is now itself a generator method (previously returned a generator)
 - exists kwarg in RegistrationClient.register_files
-- support for loading 'table' attribute as dataframe with extra ALF parts
+- support for loading 'table' attribute as data frame with extra ALF parts
 - bugfix: tag assertion should expect list of tags in cache info
 
 ## [1.17.0]
@@ -361,7 +367,7 @@ This version of ONE adds support for Alyx 2.0.0 and pandas 3.0.0 with dataset QC
 
 ### Modified
 
-- squeeze pandas dataframe on csv_read
+- squeeze pandas data frame on csv_read
 - load_cache now public method; option to load specific remote cache with tag arg
 - fix incorrect error message in one.alf.exceptions.ALFMultipleObjectsFound
 
@@ -537,7 +543,7 @@ This version of ONE adds support for Alyx 2.0.0 and pandas 3.0.0 with dataset QC
 
 ### Modified
 
-- rest command loging includes the whole json field on error
+- rest command logging includes the whole json field on error
 - added silent option to instantiate One on local files
 
 ## [1.6.0]

one/__init__.py

@@ -1,2 +1,2 @@
 """The Open Neurophysiology Environment (ONE) API."""
-__version__ = '2.11.0'
+__version__ = '2.11.1'

one/api.py

@@ -1855,8 +1855,10 @@ def list_datasets(
             return self._cache['datasets'].iloc[0:0] if details else []  # Return empty
         assert set(datasets.index.unique('eid')) == {eid}
         del filters['default_revisions_only']
+        if not keep_eid_index and 'eid' in datasets.index.names:
+            datasets = datasets.droplevel('eid')
         datasets = util.filter_datasets(
-            datasets.droplevel('eid'), assert_unique=False, wildcards=self.wildcards, **filters)
+            datasets, assert_unique=False, wildcards=self.wildcards, **filters)
         # Return only the relative path
         return datasets if details else datasets['rel_path'].sort_values().values.tolist()
 

one/tests/test_one.py

@@ -1448,6 +1448,11 @@ def test_list_datasets(self):
         self.assertEqual(183, len(dsets))  # this may change after a BWM release or patch
         self.assertEqual(1, dsets.index.nlevels, 'details data frame should be without eid index')
 
+        # Test keep_eid_index
+        dsets = self.one.list_datasets(
+            self.eid, details=True, query_type='remote', keep_eid_index=True)
+        self.assertEqual(2, dsets.index.nlevels, 'details data frame should be with eid index')
+
         # Test missing eid
         dsets = self.one.list_datasets('FMR019/2021-03-18/008', details=True, query_type='remote')
         self.assertIsInstance(dsets, pd.DataFrame)

one/webclient.py

@@ -589,7 +589,7 @@ def _generic_request(self, reqfunction, rest_query, data=None, files=None):
         rest_query = rest_query.replace(self.base_url, '')
         if not rest_query.startswith('/'):
             rest_query = '/' + rest_query
-        _logger.debug(f"{self.base_url + rest_query}, headers: {self._headers}")
+        _logger.debug(f'{self.base_url + rest_query}, headers: {self._headers}')
         headers = self._headers.copy()
         if files is None:
             data = json.dumps(data) if isinstance(data, dict) or isinstance(data, list) else data
@@ -678,8 +678,8 @@ def authenticate(self, username=None, password=None, cache_token=True, force=Fal
             rep = requests.post(self.base_url + '/auth-token', data=credentials)
         except requests.exceptions.ConnectionError:
             raise ConnectionError(
-                f"Can't connect to {self.base_url}.\n" +
-                "Check your internet connections and Alyx database firewall"
+                f'Can\'t connect to {self.base_url}.\n' +
+                'Check your internet connections and Alyx database firewall'
             )
         # Assign token or raise exception on auth error
         if rep.ok:
@@ -839,6 +839,7 @@ def download_cache_tables(self, source=None, destination=None):
 
     def _validate_file_url(self, url):
         """Asserts that URL matches HTTP_DATA_SERVER parameter.
+
         Currently only one remote HTTP server is supported for a given AlyxClient instance.  If
         the URL contains only the relative path part, the full URL is returned.
 
@@ -1069,7 +1070,7 @@ def rest(self, url=None, action=None, id=None, data=None, files=None,
                 if 'django' in kwargs.keys():
                     kwargs['django'] = kwargs['django'] + ','
                 else:
-                    kwargs['django'] = ""
+                    kwargs['django'] = ''
                 kwargs['django'] = f"{kwargs['django']}pk,{id}"
             # otherwise, look for a dictionary of filter terms
             if kwargs:
@@ -1135,7 +1136,7 @@ def json_field_write(
         # Prepare data to patch
         patch_dict = {field_name: data}
         # Upload new extended_qc to session
-        ret = self.rest(endpoint, "partial_update", id=uuid, data=patch_dict)
+        ret = self.rest(endpoint, 'partial_update', id=uuid, data=patch_dict)
         return ret[field_name]
 
     def json_field_update(
@@ -1181,7 +1182,7 @@ def json_field_update(
 
         if not isinstance(current, dict):
             _logger.warning(
-                f'Current json field {field_name} does not contains a dict, aborting update'
+                f'Current json field "{field_name}" does not contains a dict, aborting update'
             )
             return current
 
@@ -1236,7 +1237,7 @@ def json_field_remove_key(
                 f'{key}: Key not found in endpoint {endpoint} field {field_name}'
             )
             return current
-        _logger.info(f"Removing key from dict: '{key}'")
+        _logger.info(f'Removing key from dict: "{key}"')
         current.pop(key)
         # Re-write contents without removed key
         written = self.json_field_write(