From 3ec8fa71cebc6bef6ab617be564afec2c7a5dfd7 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 27 Dec 2020 01:34:08 +0100 Subject: [PATCH] convert log.warn to log.warning --- lib/galaxy/managers/licenses.py | 2 +- lib/galaxy/model/__init__.py | 2 +- lib/galaxy/objectstore/irods.py | 6 +++--- lib/galaxy/tools/error_reports/plugins/gitlab.py | 2 +- lib/galaxy/tools/parameters/dynamic_options.py | 8 ++++---- lib/galaxy/workflow/modules.py | 2 +- 6 files changed, 11 insertions(+), 11 deletions(-) diff --git a/lib/galaxy/managers/licenses.py b/lib/galaxy/managers/licenses.py index 85372eada6c..a655155e280 100644 --- a/lib/galaxy/managers/licenses.py +++ b/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 } diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index edb4ed85961..d4cc9a48c32 100644 --- a/lib/galaxy/model/__init__.py +++ b/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): diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py index eed996b37b0..898f0316ac1 100644 --- a/lib/galaxy/objectstore/irods.py +++ b/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) diff --git a/lib/galaxy/tools/error_reports/plugins/gitlab.py b/lib/galaxy/tools/error_reports/plugins/gitlab.py index 643037c1d57..136b272438f 100644 --- a/lib/galaxy/tools/error_reports/plugins/gitlab.py +++ b/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) diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py index 67bcc3fd8c8..ac6a86b2d04 100644 --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/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 = [] diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py index 6c64c9a01c1..0fff9093373 100644 --- a/lib/galaxy/workflow/modules.py +++ b/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: