Enable flake8-logging-format rules in ruff, fix G003 and G010 errors

lib/galaxy/jobs/runners/kubernetes.py

@@ -252,9 +252,8 @@ def __get_run_as_user_id(self):
                     return int(self.runner_params["k8s_run_as_user_id"])
                 except Exception:
                     log.warning(
-                        'User ID passed for Kubernetes runner needs to be an integer or "$uid", value '
-                        + self.runner_params["k8s_run_as_user_id"]
-                        + " passed is invalid"
+                        'User ID passed for Kubernetes runner needs to be an integer or "$uid", value %s passed is invalid',
+                        self.runner_params["k8s_run_as_user_id"],
                     )
                     return None
         return None
@@ -269,9 +268,8 @@ def __get_run_as_group_id(self):
                     return int(self.runner_params["k8s_run_as_group_id"])
                 except Exception:
                     log.warning(
-                        'Group ID passed for Kubernetes runner needs to be an integer or "$gid", value '
-                        + self.runner_params["k8s_run_as_group_id"]
-                        + " passed is invalid"
+                        'Group ID passed for Kubernetes runner needs to be an integer or "$gid", value %s passed is invalid',
+                        self.runner_params["k8s_run_as_group_id"],
                     )
         return None
 
@@ -284,9 +282,8 @@ def __get_supplemental_group(self):
                 return int(self.runner_params["k8s_supplemental_group_id"])
             except Exception:
                 log.warning(
-                    'Supplemental group passed for Kubernetes runner needs to be an integer or "$gid", value '
-                    + self.runner_params["k8s_supplemental_group_id"]
-                    + " passed is invalid"
+                    'Supplemental group passed for Kubernetes runner needs to be an integer or "$gid", value %s passed is invalid',
+                    self.runner_params["k8s_supplemental_group_id"],
                 )
                 return None
         return None
@@ -297,9 +294,8 @@ def __get_fs_group(self):
                 return int(self.runner_params["k8s_fs_group_id"])
             except Exception:
                 log.warning(
-                    'FS group passed for Kubernetes runner needs to be an integer or "$gid", value '
-                    + self.runner_params["k8s_fs_group_id"]
-                    + " passed is invalid"
+                    'FS group passed for Kubernetes runner needs to be an integer or "$gid", value %s passed is invalid',
+                    self.runner_params["k8s_fs_group_id"],
                 )
                 return None
         return None

lib/galaxy/metadata/set_metadata.py

@@ -262,7 +262,7 @@ def set_meta(new_dataset_instance, file_dict):
                 if not is_celery_task:
                     error_desc = "Failed to find tool_stdout or tool_stderr for this job, cannot collect metadata"
                     error_extra = f"Working dir contents [{wdc}], output directory contents [{odc}]"
-                    log.warn(f"{error_desc}. {error_extra}")
+                    log.warning(f"{error_desc}. {error_extra}")
                     raise Exception(error_desc)
                 else:
                     tool_stdout = tool_stderr = b""

lib/galaxy/visualization/plugins/config_parser.py

@@ -286,8 +286,9 @@ def parse_tests(self, xml_tree_list):
             test_result = test_elem.text.strip() if test_elem.text else None
             if not test_type or not test_result:
                 log.warning(
-                    "Skipping test. Needs both type attribute and text node to be parsed: "
-                    + f"{test_type}, {test_elem.text}"
+                    "Skipping test. Needs both type attribute and text node to be parsed: %s, %s",
+                    test_type,
+                    test_elem.text,
                 )
                 continue
             test_result = test_result.strip()

lib/galaxy/visualization/plugins/resource_parser.py

@@ -134,8 +134,11 @@ def parse_config(self, trans, param_config_dict, query_params):
 
                 except Exception as exception:
                     log.warning(
-                        "Exception parsing visualization param from query: "
-                        + f"{param_name}, {config_val}, ({str(type(exception))}) {str(exception)}"
+                        "Exception parsing visualization param from query: %s, %s, (%s) %s",
+                        param_name,
+                        config_val,
+                        type(exception),
+                        exception,
                     )
                     config_val = None
 

pyproject.toml

@@ -181,14 +181,17 @@ types-requests = "*"
 types-six = "*"
 
 [tool.ruff]
-select = ["E", "F", "B", "UP"]
+# Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),
+# flake8-logging-format (G) and pyupgrade (UP)
+select = ["E", "F", "B", "G", "UP"]
 target-version = "py37"
 # Exceptions:
 # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
 # B9 flake8-bugbear opinionated warnings
 # E402 module level import not at top of file # TODO, we would like to improve this.
 # E501 is line length (delegated to black)
-ignore = ["B008", "B9", "E402", "E501"]
+# G* are TODOs
+ignore = ["B008", "B9", "E402", "E501", "G001", "G002", "G004", "G201"]
 exclude = [
   "lib/tool_shed/test/test_data/repos"
 ]