Merge pull request galaxyproject#16915 from nsoranzo/ruff_logging_format

Enable some flake8-logging-format rules in ruff
ahmedhamidawan · Oct 25, 2023 · 7ee3412 · 7ee3412
2 parents ad6cb25 + 78e4577
commit 7ee3412
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Showing 6 changed files with 35 additions and 37 deletions.
diff --git a/lib/galaxy/jobs/runners/kubernetes.py b/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

diff --git a/lib/galaxy/metadata/set_metadata.py b/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""

diff --git a/lib/galaxy/tools/error_reports/plugins/gitlab.py b/lib/galaxy/tools/error_reports/plugins/gitlab.py
@@ -47,16 +47,16 @@ def __init__(self, **kwargs):
             self.gitlab.auth()
 
         except gitlab.GitlabAuthenticationError:
-            log.error("GitLab error reporting - Could not authenticate with GitLab.", exc_info=True)
+            log.exception("GitLab error reporting - Could not authenticate with GitLab.")
             self.gitlab = None
         except gitlab.GitlabParsingError:
-            log.error("GitLab error reporting - Could not parse GitLab message.", exc_info=True)
+            log.exception("GitLab error reporting - Could not parse GitLab message.")
             self.gitlab = None
         except (gitlab.GitlabConnectionError, gitlab.GitlabHttpError):
-            log.error("GitLab error reporting - Could not connect to GitLab.", exc_info=True)
+            log.exception("GitLab error reporting - Could not connect to GitLab.")
             self.gitlab = None
         except gitlab.GitlabError:
-            log.error("GitLab error reporting - General error communicating with GitLab.", exc_info=True)
+            log.exception("GitLab error reporting - General error communicating with GitLab.")
             self.gitlab = None
 
     def gitlab_connect(self):
@@ -195,34 +195,29 @@ def submit_report(self, dataset, job, tool, **kwargs):
                 )
 
             except gitlab.GitlabCreateError:
-                log.error("GitLab error reporting - Could not create the issue on GitLab.", exc_info=True)
+                log.exception("GitLab error reporting - Could not create the issue on GitLab.")
                 return ("Internal Error.", "danger")
             except gitlab.GitlabOwnershipError:
-                log.error(
-                    "GitLab error reporting - Could not create the issue on GitLab due to ownership issues.",
-                    exc_info=True,
-                )
+                log.exception("GitLab error reporting - Could not create the issue on GitLab due to ownership issues.")
                 return ("Internal Error.", "danger")
             except gitlab.GitlabSearchError:
-                log.error("GitLab error reporting - Could not find repository on GitLab.", exc_info=True)
+                log.exception("GitLab error reporting - Could not find repository on GitLab.")
                 return ("Internal Error.", "danger")
             except gitlab.GitlabAuthenticationError:
-                log.error("GitLab error reporting - Could not authenticate with GitLab.", exc_info=True)
+                log.exception("GitLab error reporting - Could not authenticate with GitLab.")
                 return ("Internal Error.", "danger")
             except gitlab.GitlabParsingError:
-                log.error("GitLab error reporting - Could not parse GitLab message.", exc_info=True)
+                log.exception("GitLab error reporting - Could not parse GitLab message.")
                 return ("Internal Error.", "danger")
             except (gitlab.GitlabConnectionError, gitlab.GitlabHttpError):
-                log.error("GitLab error reporting - Could not connect to GitLab.", exc_info=True)
+                log.exception("GitLab error reporting - Could not connect to GitLab.")
                 return ("Internal Error.", "danger")
             except gitlab.GitlabError:
-                log.error("GitLab error reporting - General error communicating with GitLab.", exc_info=True)
+                log.exception("GitLab error reporting - General error communicating with GitLab.")
                 return ("Internal Error.", "danger")
             except Exception:
-                log.error(
-                    "GitLab error reporting - Error reporting to GitLab had an exception that could not be "
-                    "determined.",
-                    exc_info=True,
+                log.exception(
+                    "GitLab error reporting - Error reporting to GitLab had an exception that could not be determined.",
                 )
                 return ("Internal Error.", "danger")
         else:

diff --git a/lib/galaxy/visualization/plugins/config_parser.py 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()

diff --git a/lib/galaxy/visualization/plugins/resource_parser.py b/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
 

diff --git a/pyproject.toml b/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"]
 exclude = [
   "lib/tool_shed/test/test_data/repos"
 ]