Fix broken subworkflow reodering on workflow import

We started reordering workflow steps on import in
galaxyproject#13641.

If subworkflow steps are reordered before the input connections are
set the wrong subworkflow steps are referenced when we build the
workflow connection. This broke the IWC tests for gromacs.

We now do not reorder subworkflow steps until the parent workflow is
being reordered, which is after all connections are set up.

lib/galaxy/managers/workflows.py

@@ -572,6 +572,7 @@ def build_workflow_from_raw_description(
         source=None,
         add_to_menu=False,
         hidden=False,
+        is_subworkflow=False,
     ):
         data = raw_workflow_description.as_dict
         # Put parameters in workflow mode
@@ -591,6 +592,7 @@ def build_workflow_from_raw_description(
             raw_workflow_description,
             workflow_create_options,
             name=name,
+            is_subworkflow=is_subworkflow,
         )
         if "uuid" in data:
             workflow.uuid = data["uuid"]
@@ -680,7 +682,7 @@ def update_workflow_from_raw_description(
         return workflow, errors
 
     def _workflow_from_raw_description(
-        self, trans, raw_workflow_description, workflow_state_resolution_options, name, **kwds
+        self, trans, raw_workflow_description, workflow_state_resolution_options, name, is_subworkflow=False, **kwds
     ):
         # don't commit the workflow or attach its part to the sa session - just build a
         # a transient model to operate on or render.
@@ -755,8 +757,12 @@ def _workflow_from_raw_description(
         # Second pass to deal with connections between steps
         self.__connect_workflow_steps(steps, steps_by_external_id, dry_run)
 
-        # Order the steps if possible
-        attach_ordered_steps(workflow, steps)
+        workflow.has_cycles = True
+        workflow.steps = steps
+        # we can't reorder subworkflows, as step connections would become invalid
+        if not is_subworkflow:
+            # Order the steps if possible
+            attach_ordered_steps(workflow)
 
         return workflow, missing_tool_tups
 
@@ -1637,6 +1643,7 @@ def __module_from_dict(
         steps.append(step)
         external_id = step_dict["id"]
         steps_by_external_id[external_id] = step
+        step.order_index = external_id
         if "workflow_outputs" in step_dict:
             workflow_outputs = step_dict["workflow_outputs"]
             found_output_names = set()
@@ -1703,7 +1710,11 @@ def __load_subworkflow_from_step_dict(
     def __build_embedded_subworkflow(self, trans, data, workflow_state_resolution_options):
         raw_workflow_description = self.ensure_raw_description(data)
         subworkflow = self.build_workflow_from_raw_description(
-            trans, raw_workflow_description, workflow_state_resolution_options, hidden=True
+            trans,
+            raw_workflow_description,
+            workflow_state_resolution_options,
+            hidden=True,
+            is_subworkflow=True,
         ).workflow
         return subworkflow
 

lib/galaxy/workflow/steps.py

@@ -10,11 +10,11 @@
 )
 
 
-def attach_ordered_steps(workflow, steps):
+def attach_ordered_steps(workflow):
     """Attempt to topologically order steps and attach to workflow. If this
     fails - the workflow contains cycles so it mark it as such.
     """
-    ordered_steps = order_workflow_steps(steps)
+    ordered_steps = order_workflow_steps(workflow.steps)
     workflow.has_cycles = True
     if ordered_steps:
         workflow.has_cycles = False
@@ -30,6 +30,8 @@ def order_workflow_steps(steps):
     """
     position_data_available = bool(steps)
     for step in steps:
+        if step.subworkflow:
+            attach_ordered_steps(step.subworkflow)
         if not step.position or "left" not in step.position or "top" not in step.position:
             position_data_available = False
     if position_data_available: