Record input parameter invocation inputs

as they become available. Fixes the test in in the previous commit and
also means that inputs are properly recorded, something that's always
been unavailable for subworkflow invocations.

lib/galaxy/workflow/modules.py

@@ -1029,13 +1029,6 @@ class InputModule(WorkflowModule):
                     step_outputs["input_ds_copy"] = new_hdca
                 else:
                     raise Exception("Unknown history content encountered")
-        # If coming from UI - we haven't registered invocation inputs yet,
-        # so do that now so dependent steps can be recalculated. In the future
-        # everything should come in from the API and this can be eliminated.
-        if not invocation.has_input_for_step(step.id):
-            content = next(iter(step_outputs.values()))
-            if content and content is not NO_REPLACEMENT:
-                invocation.add_input(content, step.id)
         progress.set_outputs_for_input(invocation_step, step_outputs)
         return None
 

lib/galaxy/workflow/run.py

@@ -623,6 +623,12 @@ class WorkflowProgress:
 
         if step.label and step.type == "parameter_input" and "output" in outputs:
             self.runtime_replacements[step.label] = str(outputs["output"])
+        invocation = invocation_step.workflow_invocation
+        if not invocation.has_input_for_step(step.id):
+            content = outputs.get("output", NO_REPLACEMENT)
+            if content is not NO_REPLACEMENT:
+                log.info("ADDING INPUT FOR STEP %s: %s", step.id, content, exc_info=True)
+                invocation.add_input(content, step.id)
         self.set_step_outputs(invocation_step, outputs, already_persisted=already_persisted)
 
     def effective_replacement_dict(self):

test/unit/workflows/test_workflow_progress.py

@@ -94,8 +94,7 @@ class TestWorkflowProgress(TestCase):
                 workflow_invocation_step.state = "scheduled"
                 workflow_invocation_step.workflow_step = self._step(i)
                 assert step_id == self._step(i).id
-                # workflow_invocation_step.workflow_invocation = self.invocation
-                self.invocation.steps.append(workflow_invocation_step)
+                workflow_invocation_step.workflow_invocation = self.invocation
 
             workflow_invocation_step_state = model.WorkflowRequestStepState()
             workflow_invocation_step_state.workflow_step_id = step_id
@@ -111,6 +110,7 @@ class TestWorkflowProgress(TestCase):
         else:
             workflow_invocation_step = model.WorkflowInvocationStep()
             workflow_invocation_step.workflow_step = self._step(index)
+            workflow_invocation_step.workflow_invocation = self.invocation
             return workflow_invocation_step
 
     def test_connect_data_input(self):
@@ -211,6 +211,7 @@ class TestWorkflowProgress(TestCase):
         subworkflow_invocation_step.workflow_step_id = subworkflow_input_step.id
         subworkflow_invocation_step.state = "new"
         subworkflow_invocation_step.workflow_step = subworkflow_input_step
+        subworkflow_invocation_step.workflow_invocation = subworkflow_invocation
 
         subworkflow_progress.set_outputs_for_input(subworkflow_invocation_step)