Fix running subworkflows with disconnected optional/default inputs

lib/galaxy/model/__init__.py

@@ -7050,6 +7050,10 @@ class WorkflowStep(Base, RepresentById):
         self.uuid = uuid4()
         self._input_connections_by_name = None
 
+    @reconstructor
+    def init_on_load(self):
+        self._input_connections_by_name = None
+
     @property
     def tool_uuid(self):
         return self.dynamic_tool and self.dynamic_tool.uuid

lib/galaxy/workflow/run.py

@@ -466,9 +466,9 @@ class WorkflowProgress:
         subworkflow_inputs = {}
         for input_subworkflow_step in subworkflow.input_steps:
             connection_found = False
+            subworkflow_step_id = input_subworkflow_step.id
             for input_connection in step.input_connections:
-                if input_connection.input_subworkflow_step == input_subworkflow_step:
-                    subworkflow_step_id = input_subworkflow_step.id
+                if input_connection.input_subworkflow_step_id == subworkflow_step_id:
                     is_data = input_connection.output_step.type != "parameter_input"
                     replacement = self.replacement_for_connection(
                         input_connection,
@@ -478,7 +478,7 @@ class WorkflowProgress:
                     connection_found = True
                     break
 
-            if not connection_found:
+            if not connection_found and not input_subworkflow_step.input_optional:
                 raise Exception("Could not find connections for all subworkflow inputs.")
 
         return WorkflowProgress(subworkflow_invocation, subworkflow_inputs, self.module_injector, param_map=param_map)

test/unit/workflows/test_workflow_progress.py

@@ -189,6 +189,8 @@ class WorkflowProgressTestCase(unittest.TestCase):
         subworkflow_invocation = self.invocation.create_subworkflow_invocation_for_step(
             self.invocation.workflow.step_by_index(1)
         )
+        self.app.model.session.add(subworkflow_invocation)
+        self.app.model.session.flush()
         progress = self._new_workflow_progress()
         remaining_steps = progress.remaining_steps()
         (subworkflow_step, subworkflow_invocation_step) = remaining_steps[0]