convert log.warn to log.warning

lib/galaxy/managers/licenses.py

@@ -53,7 +53,7 @@ class LicensesManager:
         if uri in self._by_index:
             return self._by_index[uri]
         else:
-            log.warn("Unknown license URI encountered [%s]" % uri)
+            log.warning("Unknown license URI encountered [%s]" % uri)
         return {
             "url": uri
         }

lib/galaxy/model/__init__.py

@@ -3908,7 +3908,7 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, RepresentById):
             ''').execution_options(autocommit=True)
         ret = object_session(self).execute(sql, {'library_dataset_id': ldda.library_dataset_id, 'ldda_id': ldda.id})
         if ret.rowcount < 1:
-            log.warn(f'Attempt to updated parent folder times failed: {ret.rowcount} records updated.')
+            log.warning(f'Attempt to updated parent folder times failed: {ret.rowcount} records updated.')
 
 
 class ExtendedMetadata(RepresentById):

lib/galaxy/objectstore/irods.py

@@ -307,7 +307,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
             data_obj = self.session.data_objects.get(data_object_path)
             return data_obj.__sizeof__()
         except (DataObjectDoesNotExist, CollectionDoesNotExist):
-            log.warn("Collection or data object (%s) does not exist", data_object_path)
+            log.warning("Collection or data object (%s) does not exist", data_object_path)
             return -1
         except NetworkException as e:
             log.exception(e)
@@ -369,7 +369,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         try:
             data_obj = self.session.data_objects.get(data_object_path)
         except (DataObjectDoesNotExist, CollectionDoesNotExist):
-            log.warn("Collection or data object (%s) does not exist", data_object_path)
+            log.warning("Collection or data object (%s) does not exist", data_object_path)
             return False
         except NetworkException as e:
             log.exception(e)
@@ -566,7 +566,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
                 try:
                     col = self.session.collections.get(col_path)
                 except CollectionDoesNotExist:
-                    log.warn("Collection (%s) does not exist!", col_path)
+                    log.warning("Collection (%s) does not exist!", col_path)
                     return False
                 except NetworkException as e:
                     log.exception(e)

lib/galaxy/tools/error_reports/plugins/gitlab.py

@@ -124,7 +124,7 @@ class GitLabPlugin(BaseGitPlugin):
                         self.git_project_cache[gitlab_projecturl] = self.gitlab.projects.get(gitlab_urlencodedpath)
                 except gitlab.GitlabGetError:
                     # Handle scenario where the repository doesn't exist so we can still continue
-                    log.warn("GitLab error reporting - Repository '%s' doesn't exist, using default repository." % gitlab_urlencodedpath)
+                    log.warning("GitLab error reporting - Repository '%s' doesn't exist, using default repository." % gitlab_urlencodedpath)
                     # Redo some of the previous steps to recover from such an issue but continue issue creation
                     gitlab_projecturl = "/".join((self.git_default_repo_owner, self.git_default_repo_name))
                     gitlab_urlencodedpath = urllib.quote_plus(gitlab_projecturl)

lib/galaxy/tools/parameters/dynamic_options.py

@@ -189,10 +189,10 @@ class DataMetaFilter(Filter):
         try:
             ref = _get_ref_data(other_values, self.ref_name)
         except KeyError:  # no such dataset
-            log.warn("could not filter by metadata: %s unknown" % self.ref_name)
+            log.warning("could not filter by metadata: %s unknown" % self.ref_name)
             return []
         except ValueError:  # not a valid dataset
-            log.warn("could not filter by metadata: %s not a data or collection parameter" % self.ref_name)
+            log.warning("could not filter by metadata: %s not a data or collection parameter" % self.ref_name)
             return []
         # get the metadata value.
         # - for lists: (of data sets) and collections the meta data values of all
@@ -661,10 +661,10 @@ class DynamicOptions:
             try:
                 datasets = _get_ref_data(other_values, self.dataset_ref_name)
             except KeyError:  # no such dataset
-                log.warn("could not create dynamic options from_dataset: %s unknown" % self.dataset_ref_name)
+                log.warning("could not create dynamic options from_dataset: %s unknown" % self.dataset_ref_name)
                 return []
             except ValueError:  # not a valid dataset
-                log.warn("could not create dynamic options from_dataset: %s not a data or collection parameter" % self.dataset_ref_name)
+                log.warning("could not create dynamic options from_dataset: %s not a data or collection parameter" % self.dataset_ref_name)
                 return []
 
             options = []

lib/galaxy/workflow/modules.py

@@ -1170,7 +1170,7 @@ class InputParameterModule(WorkflowModule):
                     suggestion_values = restrictions_cond_values["suggestions"]
                     rval.update({"suggestions": _string_to_parameter_def_option(suggestion_values)})
                 else:
-                    log.warn("Unknown restriction conditional type encountered for workflow parameter.")
+                    log.warning("Unknown restriction conditional type encountered for workflow parameter.")
 
             rval.update({"parameter_type": parameters_def["parameter_type"], "optional": optional})
         else: