Stronger typing around galaxy exceptions.

Fix err_msg issue.
jmchilton · Mar 29, 2023 · 7209c8d · 7209c8d
1 parent 1e27fe4
commit 7209c8d
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 7 deletions.
diff --git a/lib/galaxy/exceptions/__init__.py b/lib/galaxy/exceptions/__init__.py
@@ -15,6 +15,7 @@
 have nothing to do with the web - keep this in mind when defining exception names
 and messages.
 """
+from typing import Optional
 
 from .error_codes import (
     error_codes_by_name,
@@ -25,26 +26,27 @@
 class MessageException(Exception):
     """Most generic Galaxy exception - indicates merely that some exceptional condition happened."""
 
+    err_msg: str
     # status code to be set when used with API.
     status_code: int = 400
     # Error code information embedded into API json responses.
     err_code: ErrorCode = error_codes_by_name["UNKNOWN"]
 
-    def __init__(self, err_msg=None, type="info", **extra_error_info):
+    def __init__(self, err_msg: Optional[str] = None, type="info", **extra_error_info):
         self.err_msg = err_msg or self.err_code.default_error_message
         self.type = type
         self.extra_error_info = extra_error_info
 
     @staticmethod
-    def from_code(status_code, message):
+    def from_code(status_code: int, message: Optional[str]) -> "MessageException":
         exception_class = MessageException
         if status_code == 404:
             exception_class = ObjectNotFound
         elif status_code / 100 == 5:
             exception_class = InternalServerError
         return exception_class(message)
 
-    def __str__(self):
+    def __str__(self) -> str:
         return self.err_msg
 
 

diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
@@ -2514,9 +2514,9 @@ def populate_module_and_state(
         if step_errors:
             raise exceptions.MessageException(step_errors, err_data={step.order_index: step_errors})
         if step.upgrade_messages:
+            upgrade_messages = step.upgrade_messages
+            error_message = f'Workflow step "{step.id}" had upgrade messages: {upgrade_messages}'
             if allow_tool_state_corrections:
-                log.debug('Workflow step "%i" had upgrade messages: %s', step.id, step.upgrade_messages)
+                log.debug(error_message)
             else:
-                raise exceptions.MessageException(
-                    step.upgrade_messages, err_data={step.order_index: step.upgrade_messages}
-                )
+                raise exceptions.MessageException(error_message, err_data={step.order_index: upgrade_messages})