From 5050ccde3df7113846e83d567d38194d783f26e2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 27 Jun 2024 14:54:55 +0200
Subject: [PATCH 1/2] Add test to make sure when_expression is not lost on
 refactoring

---
 test/integration/test_workflow_refactoring.py | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/test/integration/test_workflow_refactoring.py b/test/integration/test_workflow_refactoring.py
index 6a03d818ce31..d2501090aeef 100644
--- a/test/integration/test_workflow_refactoring.py
+++ b/test/integration/test_workflow_refactoring.py
@@ -537,6 +537,33 @@ def test_tool_version_upgrade_no_state_change(self):
         assert len(action_executions[0].messages) == 0
         assert self._latest_workflow.step_by_label("the_step").tool_version == "0.2"
 
+    def test_tool_version_upgrade_keeps_when_expression(self):
+        self.workflow_populator.upload_yaml_workflow(
+            """
+class: GalaxyWorkflow
+inputs:
+  the_bool:
+    type: boolean
+steps:
+  the_step:
+    tool_id: multiple_versions
+    tool_version: '0.1'
+    state:
+      inttest: 0
+    when: $inputs.the_bool
+"""
+        )
+        assert self._latest_workflow.step_by_label("the_step").tool_version == "0.1"
+        actions: ActionsJson = [
+            {"action_type": "upgrade_tool", "step": {"label": "the_step"}},
+        ]
+        action_executions = self._refactor(actions).action_executions
+        assert len(action_executions) == 1
+        assert len(action_executions[0].messages) == 0
+        step = self._latest_workflow.step_by_label("the_step")
+        assert step.tool_version == "0.2"
+        assert step.when_expression
+
     def test_tool_version_upgrade_state_added(self):
         self.workflow_populator.upload_yaml_workflow(
             """

From ed8dc4b8e29db41993316bf4a65591e73f264219 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 27 Jun 2024 14:54:23 +0200
Subject: [PATCH 2/2] Fix dropped when_expression on workflow/tool_upgrade

Fixes https://github.com/galaxyproject/galaxy/issues/18441
---
 lib/galaxy/workflow/refactor/execute.py       | 3 +++
 test/integration/test_workflow_refactoring.py | 4 +++-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/workflow/refactor/execute.py b/lib/galaxy/workflow/refactor/execute.py
index d35cbbbc7785..2582380fc623 100644
--- a/lib/galaxy/workflow/refactor/execute.py
+++ b/lib/galaxy/workflow/refactor/execute.py
@@ -531,6 +531,9 @@ def _patch_step(self, execution, step, step_def):
                 if upgrade_input["name"] == input_name:
                     matching_input = upgrade_input
                     break
+                elif step.when_expression and f"inputs.{input_name}" in step.when_expression:
+                    # TODO: eventually track step inputs more formally
+                    matching_input = upgrade_input
 
             # In the future check parameter type, format, mapping status...
             if matching_input is None:
diff --git a/test/integration/test_workflow_refactoring.py b/test/integration/test_workflow_refactoring.py
index d2501090aeef..d68b8916145b 100644
--- a/test/integration/test_workflow_refactoring.py
+++ b/test/integration/test_workflow_refactoring.py
@@ -548,9 +548,11 @@ def test_tool_version_upgrade_keeps_when_expression(self):
   the_step:
     tool_id: multiple_versions
     tool_version: '0.1'
+    in:
+      when: the_bool
     state:
       inttest: 0
-    when: $inputs.the_bool
+    when: $(inputs.when)
 """
         )
         assert self._latest_workflow.step_by_label("the_step").tool_version == "0.1"