WIP:CWL default file value_from work

lib/galaxy/managers/workflows.py

@@ -1782,11 +1782,14 @@ def __module_from_dict(
                 step_input.merge_type = input_dict.get("merge_type", step_input.default_merge_type)
                 step_input.scatter_type = input_dict.get("scatter_type", step_input.default_scatter_type)
                 value_from = input_dict.get("value_from", None)
-                if value_from is None:
-                    # Super hacky - we probably need distinct value from and
-                    # default handling.
-                    value_from = input_dict.get("default")
+                # if value_from is None:
+                #     # Super hacky - we probably need distinct value from and
+                #     # default handling.
+                #     value_from = input_dict.get("default")
                 step_input.value_from = value_from
+                step_input.default_value = input_dict.get("default")
+                if step_input.default_value:
+                    step_input.default_value_set = True
 
         # Create the model class for the step
         steps.append(step)

lib/galaxy/workflow/modules.py

@@ -124,7 +124,7 @@ class ConditionalStepWhen(BooleanToolParameter):
     pass
 
 
-def to_cwl(value, hda_references, step):
+def to_cwl(value, hda_references, step, require_ok=True):
     element_identifier = None
     if isinstance(value, model.DatasetCollectionElement) and value.hda:
         element_identifier = value.element_identifier
@@ -135,7 +135,8 @@ def to_cwl(value, hda_references, step):
         if not value.dataset.in_ready_state():
             why = "dataset [%s] is needed for valueFrom expression and is non-ready" % value.id
             raise DelayedWorkflowEvaluation(why=why)
-        if not value.is_ok:
+        if require_ok and not value.is_ok:
+            # materialize and delay ?
             raise FailWorkflowEvaluation(
                 why=InvocationFailureDatasetFailed(
                     reason=FailureReason.dataset_failed, hda_id=value.id, workflow_step_id=step.id
@@ -2209,14 +2210,17 @@ def decode_runtime_state(self, step, runtime_state):
                 f"Tool {self.tool_id} missing. Cannot recover runtime state.", tool_id=self.tool_id
             )
 
-    def evaluate_value_from_expressions(self, progress, step, execution_state, extra_step_state):
+    def evaluate_value_from_expressions(self, progress, step, execution_state, extra_step_state, use_default=False):
         value_from_expressions = {}
         replacements: Dict = {}
 
         for key in execution_state.inputs.keys():
             step_input = step.inputs_by_name.get(key)
-            if step_input and step_input.value_from is not None:
-                value_from_expressions[key] = step_input.value_from
+            if step_input:
+                if step_input.value_from is not None and not use_default:
+                    value_from_expressions[key] = step_input.value_from
+                else:
+                    value_from_expressions[key] = step_input.default_value
 
         if not value_from_expressions:
             return replacements
@@ -2226,7 +2230,8 @@ def evaluate_value_from_expressions(self, progress, step, execution_state, extra
         for key, value in extra_step_state.items():
             step_state[key] = to_cwl(value, hda_references=hda_references, step=step)
         for key, value in execution_state.inputs.items():
-            step_state[key] = to_cwl(value, hda_references=hda_references, step=step)
+            # require_ok = False for deferred datasets ... might instead need to materialize ??
+            step_state[key] = to_cwl(value, hda_references=hda_references, step=step, require_ok=False)
 
         for key, value_from in value_from_expressions.items():
             as_cwl_value = do_eval(
@@ -2373,11 +2378,14 @@ def callback(input, prefixed_name, **kwargs):
                 execution_state.inputs["__when_value__"] = when_value
 
             unmatched_input_connections = expected_replacement_keys - found_replacement_keys
+            use_default = False
             if unmatched_input_connections:
                 log.warning(f"Failed to use input connections for inputs [{unmatched_input_connections}]")
+                # Hack
+                use_default=True
 
             expression_replacements = self.evaluate_value_from_expressions(
-                progress, step, execution_state, extra_step_state
+                progress, step, execution_state, extra_step_state, use_default=True
             )
 
             def expression_callback(input, prefixed_name, **kwargs):

lib/galaxy/workflow/run.py

@@ -535,16 +535,24 @@ def replacement_for_input(self, trans, step: "WorkflowStep", input_dict: Dict[st
                 else:
                     replacement = temp
             else:
+                if is_data:
+                    for step_input in step.inputs:
+                        if step_input.name == prefixed_name and step_input.value_from:
+                            log.debug("THIS?")
+                            log.debug("GOT DEFAULT VALUE %s, value_from %s", step_input.default_value, step_input.value_from)
+                            return raw_to_galaxy(trans.app, trans.history, step_input.value_from)
                 replacement = self.replacement_for_input_connections(
                     step,
                     input_dict,
                     connection,
                 )
         else:
             for step_input in step.inputs:
-                if step_input.name == prefixed_name and step_input.default_value_set:
+                if step_input.name == prefixed_name:
+                    log.debug("GOT DEFAULT VALUE %s, value_from %s", step_input.default_value, step_input.value_from)
+                if step_input.name == prefixed_name and (step_input.default_value or step_input.value_from):
                     if is_data:
-                        replacement = raw_to_galaxy(trans.app, trans.history, step_input.default_value)
+                        replacement = raw_to_galaxy(trans.app, trans.history, step_input.value_from or step_input.default_value)
         return replacement
 
     def replacement_for_connection(self, connection: "WorkflowStepConnection", is_data: bool = True) -> Any: