From 6b3d13e4270a773835e8662dd4e42fc23a56367c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 14 Nov 2020 23:15:40 +0100
Subject: [PATCH] Recover step output value

in WorkflowProgress instance. Fixes running subworkflows with
parameter_input steps.
Fixes https://github.com/galaxyproject/galaxy/issues/8390 and
allows us to get rid of one FIXME I added when working around
https://github.com/galaxyproject/galaxy/issues/8248.
---
 lib/galaxy/model/mapping.py |  8 ++++++++
 lib/galaxy/workflow/run.py  | 16 ++++++----------
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 38622dc1f3b..48ae5cf0ebf 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -2625,6 +2625,14 @@ simple_mapping(
 simple_mapping(
     model.WorkflowInvocationOutputValue,
     workflow_invocation=relation(model.WorkflowInvocation, backref="output_values"),
+    workflow_invocation_step=relation(model.WorkflowInvocationStep,
+        foreign_keys=[model.WorkflowInvocationStep.table.c.workflow_invocation_id, model.WorkflowInvocationStep.table.c.workflow_step_id],
+        primaryjoin=and_(
+            model.WorkflowInvocationStep.table.c.workflow_invocation_id == model.WorkflowInvocationOutputValue.table.c.workflow_invocation_id,
+            model.WorkflowInvocationStep.table.c.workflow_step_id == model.WorkflowInvocationOutputValue.table.c.workflow_step_id,
+        ),
+        backref='output_value'
+    ),
     workflow_step=relation(model.WorkflowStep),
     workflow_output=relation(model.WorkflowOutput),
 )
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index 35938c3ca36..b4bdeda6187 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -352,16 +352,10 @@ class WorkflowProgress:
         try:
             replacement = step_outputs[output_name]
         except KeyError:
-            replacement = self.inputs_by_step_id.get(output_step_id)
-            if connection.output_step.type == 'parameter_input' and output_step_id is not None:
-                # FIXME: parameter_input step outputs should be properly recorded as step outputs, but for now we can
-                # short-circuit and just pick the input value
-                pass
-            else:
-                # Must resolve.
-                template = "Workflow evaluation problem - failed to find output_name %s in step_outputs %s"
-                message = template % (output_name, step_outputs)
-                raise Exception(message)
+            # Must resolve.
+            template = "Workflow evaluation problem - failed to find output_name %s in step_outputs %s"
+            message = template % (output_name, step_outputs)
+            raise Exception(message)
         if isinstance(replacement, model.HistoryDatasetCollectionAssociation):
             if not replacement.collection.populated:
                 if not replacement.waiting_for_elements:
@@ -428,6 +422,8 @@ class WorkflowProgress:
 
     def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
         step = invocation_step.workflow_step
+        if invocation_step.output_value:
+            outputs[invocation_step.output_value.workflow_output.output_name] = invocation_step.output_value.value
         self.outputs[step.id] = outputs
         if not already_persisted:
             for output_name, output_object in outputs.items():