From da3a8a498538842acf05dc21922fa45ac6d9353f Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 5 Aug 2024 11:06:14 -0400
Subject: [PATCH] Improve tool shed API error messages for repo path bug.

---
 lib/galaxy/exceptions/__init__.py      | 5 +++++
 lib/galaxy/exceptions/error_codes.json | 5 +++++
 lib/tool_shed/managers/tools.py        | 5 +++++
 3 files changed, 15 insertions(+)

diff --git a/lib/galaxy/exceptions/__init__.py b/lib/galaxy/exceptions/__init__.py
index 8deab77bc17b..82f66efdbe7d 100644
--- a/lib/galaxy/exceptions/__init__.py
+++ b/lib/galaxy/exceptions/__init__.py
@@ -250,6 +250,11 @@ class InconsistentDatabase(MessageException):
     err_code = error_codes_by_name["INCONSISTENT_DATABASE"]
 
 
+class InconsistentApplicationState(MessageException):
+    status_code = 500
+    err_code = error_codes_by_name["INCONSISTENT_APPLICATION_STATE"]
+
+
 class InternalServerError(MessageException):
     status_code = 500
     err_code = error_codes_by_name["INTERNAL_SERVER_ERROR"]
diff --git a/lib/galaxy/exceptions/error_codes.json b/lib/galaxy/exceptions/error_codes.json
index 99464306acb6..e148b102b786 100644
--- a/lib/galaxy/exceptions/error_codes.json
+++ b/lib/galaxy/exceptions/error_codes.json
@@ -189,6 +189,11 @@
         "code": 500006,
         "message": "Reference data required for program execution failed to load."
     },
+    {
+        "name": "INCONSISTENT_APPLICATION_STATE",
+        "code": 500007,
+        "message": "Inconsistent application state (likely not dbms related) prevented fulfilling the request."
+    },
     {
         "name": "NOT_IMPLEMENTED",
         "code": 501001,
diff --git a/lib/tool_shed/managers/tools.py b/lib/tool_shed/managers/tools.py
index b9dc6209e1b3..f569935d51ee 100644
--- a/lib/tool_shed/managers/tools.py
+++ b/lib/tool_shed/managers/tools.py
@@ -10,6 +10,7 @@
 
 from galaxy import exceptions
 from galaxy.exceptions import (
+    InconsistentApplicationState,
     InternalServerError,
     ObjectNotFound,
     RequestParameterInvalidException,
@@ -149,8 +150,12 @@ def _shed_tool_source_for(
         if error_message:
             raise InternalServerError("Failed to materialize target repository revision")
         repo_files_dir = repository_metadata.repository.repo_path(trans.app)
+        if not repo_files_dir:
+            raise InconsistentApplicationState(f"Failed to resolve repository path from hgweb_config_manager for [{trs_tool_id}], inconsistent repository state or application configuration")
         repo_rel_tool_path = relpath(tool_config, repo_files_dir)
         path_to_tool = os.path.join(work_dir, repo_rel_tool_path)
+        if not os.path.exists(path_to_tool):
+            raise InconsistentApplicationState(f"Target tool expected at [{path_to_tool}] and not found, inconsistent repository state or application configuration")
         tool_source = get_tool_source(path_to_tool)
         return tool_source
     finally: