Merge pull request #14494 from mvdbeek/fix_refactor_action

[22.05] Fix refactor action dropping outputs on subworkflow connection

lib/galaxy/workflow/modules.py

@@ -540,7 +540,12 @@ class SubWorkflowModule(WorkflowModule):
                             data_output["name"] == workflow_output["output_name"]
                             or data_output_uuid == workflow_output_uuid
                         ):
-                            data_output["label"] = label
+                            change_datatype_action = step["post_job_actions"].get(
+                                f"ChangeDatatypeAction{data_output['name']}"
+                            )
+                            if change_datatype_action:
+                                self.post_job_actions[f"ChangeDatatypeAction{label}"] = change_datatype_action
+                            data_output["name"] = label
                             # That's the right data_output
                             break
                     else:
@@ -551,15 +556,7 @@ class SubWorkflowModule(WorkflowModule):
                             f"Workflow output '{workflow_output['output_name']}' defined, but not listed among data outputs"
                         )
                         continue
-                    post_job_actions = step["post_job_actions"].copy()
-                    change_datatype_action = post_job_actions.pop(f"ChangeDatatypeAction{data_output['name']}", None)
-                    # Post job actions are referred to by tool output name,
-                    # but that's not guaranteed to be unique within a workflow,
-                    # but the label is unique.
-                    if change_datatype_action:
-                        post_job_actions[f"ChangeDatatypeAction{label}"] = change_datatype_action
 
-                    self.post_job_actions.update(post_job_actions)
                     outputs.append(data_output)
         return outputs
 

lib/galaxy/workflow/refactor/execute.py

@@ -517,7 +517,7 @@ class WorkflowRefactorExecutor:
         # TODO: find workflow outputs that need to be dropped and report them
         upgrade_inputs = step.module.get_all_inputs()
         upgrade_outputs = step.module.get_all_outputs()
-        upgrade_output_names = [u.get("label") or u["name"] for u in upgrade_outputs]
+        upgrade_output_names = {u["name"] for u in upgrade_outputs}
         upgrade_order_index = step_def["id"]
         upgrade_label = step_def.get("label")
         all_input_connections = step_def.get("input_connections")

lib/galaxy_test/selenium/test_workflow_editor.py

@@ -587,8 +587,8 @@ steps:
         node.output_data_row(output_name="workflow_output", extension="bam").wait_for_visible()
         # Move canvas, so terminals are in viewport
         self.move_center_of_canvas(xoffset=100, yoffset=100)
-        self.workflow_editor_connect("nested_workflow#out_file1", "metadata_bam#input_bam")
-        self.assert_connected("nested_workflow#out_file1", "metadata_bam#input_bam")
+        self.workflow_editor_connect("nested_workflow#workflow_output", "metadata_bam#input_bam")
+        self.assert_connected("nested_workflow#workflow_output", "metadata_bam#input_bam")
 
     @selenium_test
     def test_editor_duplicate_node(self):

test/unit/workflows/test_modules.py

@@ -244,9 +244,9 @@ def test_subworkflow_new_outputs():
     outputs = subworkflow_module.get_data_outputs()
     assert len(outputs) == 2, len(outputs)
     output1, output2 = outputs
-    assert output1["label"] == "out1"
+    assert output1["name"] == "out1"
     assert output1["extensions"] == ["input"]
-    assert output2["label"] == "4:out_file1", output2["label"]
+    assert output2["name"] == "4:out_file1", output2["name"]
 
 
 class MapOverTestCase(NamedTuple):