From 07b38ba429e8b04719d070b9e7a7763dce043355 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 15 Sep 2022 14:42:50 +0200
Subject: [PATCH] Fix `toolbox` access in invocation export

When exporting an invocation using Celery we don't have access to the ToolBox and also don't need it so we make it optional.
Thanks Marius for the solution.

In addition:
- Fix mypy by raising a tool missing exception in the `augment` method
- Also remove unused `inputs` parameter

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 lib/galaxy/workflow/modules.py | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index ca0d8783a53..e3dd5e35c7f 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -1437,9 +1437,11 @@ class ToolModule(WorkflowModule):
         self.tool_id = tool_id
         self.tool_version = str(tool_version) if tool_version else None
         self.tool_uuid = tool_uuid
-        self.tool = trans.app.toolbox.get_tool(
-            tool_id, tool_version=tool_version, exact=exact_tools, tool_uuid=tool_uuid
-        )
+        self.tool = None
+        if getattr(trans.app, "toolbox", None):
+            self.tool = trans.app.toolbox.get_tool(
+                tool_id, tool_version=tool_version, exact=exact_tools, tool_uuid=tool_uuid
+            )
         if self.tool:
             current_tool_id = self.tool.id
             current_tool_version = str(self.tool.version)
@@ -1789,7 +1791,12 @@ class ToolModule(WorkflowModule):
         input_connections = kwds.get("input_connections", {})
         expected_replacement_keys = input_connections.keys()
 
-        def augment(expected_replacement_key, inputs, inputs_states):
+        def augment(expected_replacement_key, inputs_states):
+            if self.tool is None:
+                raise ToolMissingException(
+                    f"Tool {self.tool_id} missing. Cannot augment tool state for input connections.",
+                    tool_id=self.tool_id,
+                )
             if "|" not in expected_replacement_key:
                 return
 
@@ -1817,12 +1824,11 @@ class ToolModule(WorkflowModule):
 
             if repeat_instance_state:
                 # TODO: untest branch - no test case for nested repeats yet...
-                augment(rest, repeat.inputs, repeat_instance_state)
+                augment(rest, repeat_instance_state)
 
         for expected_replacement_key in expected_replacement_keys:
             inputs_states = self.state.inputs
-            inputs = self.tool.inputs
-            augment(expected_replacement_key, inputs, inputs_states)
+            augment(expected_replacement_key, inputs_states)
 
     def get_runtime_state(self):
         state = DefaultToolState()
@@ -2097,7 +2103,7 @@ class WorkflowModuleFactory:
 
     def from_workflow_step(self, trans, step, **kwargs):
         """
-        Return module initializd from the WorkflowStep object `step`.
+        Return module initialized from the WorkflowStep object `step`.
         """
         type = step.type
         return self.module_types[type].from_workflow_step(trans, step, **kwargs)