Allow workflow inputs to be specifiable by UUID without explicit inputs_by.

Since there is no chance of conflict with step.id or step.order_index, just allow inputs or ds_map respectively to be indexed by UUID.

lib/galaxy/workflow/run_request.py

@@ -53,18 +53,25 @@ def normalize_inputs(steps, inputs, inputs_by):
         if step.type not in INPUT_STEP_TYPES:
             continue
 
-        if inputs_by == "step_id":
-            inputs_key = str( step.id )
-        elif inputs_by == "step_index":
-            inputs_key = str( step.order_index )
-        elif inputs_by == "step_uuid":
-            inputs_key = str( step.uuid )
-        elif inputs_by == "name":
-            inputs_key = step.tool_inputs.get( 'name', None )
-        else:
-            message = "Workflow cannot be run because unexpected inputs_by value specified."
-            raise exceptions.MessageException( message )
-        if inputs_key not in inputs:
+        possible_input_keys = []
+        for inputs_by_el in inputs_by.split("|"):
+            if inputs_by_el == "step_id":
+                possible_input_keys = [str( step.id )]
+            elif inputs_by_el == "step_index":
+                possible_input_keys = [str( step.order_index )]
+            elif inputs_by_el == "step_uuid":
+                possible_input_keys = [str( step.uuid )]
+            elif inputs_by_el == "name":
+                possible_input_keys = [step.tool_inputs.get( 'name', None )]
+            else:
+                message = "Workflow cannot be run because unexpected inputs_by value specified."
+                raise exceptions.MessageException( message )
+        inputs_key = None
+        for possible_input_key in possible_input_keys:
+            if possible_input_key in inputs:
+                inputs_key = possible_input_key
+
+        if not inputs_key:
             message = "Workflow cannot be run because an expected input step '%s' has no input dataset." % step.id
             raise exceptions.MessageException( message )
 
@@ -164,18 +171,13 @@ def build_workflow_run_config( trans, workflow, payload ):
         # Default to legacy behavior - read ds_map and reference steps
         # by unencoded step id (a raw database id).
         inputs = payload.get( 'ds_map', {} )
-        inputs_by = inputs_by or 'step_id'
+        inputs_by = inputs_by or 'step_id|step_uuid'
     else:
         inputs = inputs or {}
         # New default is to reference steps by index of workflow step
         # which is intrinsic to the workflow and independent of the state
         # of Galaxy at the time of workflow import.
-        inputs_by = inputs_by or 'step_index'
-
-        # TODO: with a little reworking this default could be
-        # step_index or step_uuid depending on what is inputs -
-        # unlike step_id and step_index there is not chance of
-        # conflicts.
+        inputs_by = inputs_by or 'step_index|step_uuid'
 
     add_to_history = 'no_add_to_history' not in payload
     history_param = payload.get('history', '')

test/api/test_workflows.py

@@ -78,13 +78,14 @@ class BaseWorkflowsApiTestCase( api.ApiTestCase ):
         elif inputs_by == "name":
             workflow_request[ "inputs" ] = dumps( label_map )
             workflow_request[ "inputs_by" ] = 'name'
-        elif inputs_by == "step_uuid":
+        elif inputs_by in [ "step_uuid", "uuid_implicitly" ]:
             uuid_map = {
                 workflow["steps"]["0"]["uuid"]: self._ds_entry(hda1),
                 workflow["steps"]["1"]["uuid"]: self._ds_entry(hda2),
             }
             workflow_request[ "inputs" ] = dumps( uuid_map )
-            workflow_request[ "inputs_by" ] = "step_uuid"
+            if inputs_by == "step_uuid":
+                workflow_request[ "inputs_by" ] = "step_uuid"
 
         return workflow_request, history_id
 
@@ -431,6 +432,10 @@ class WorkflowsApiTestCase( BaseWorkflowsApiTestCase ):
     def test_run_workflow_by_uuid( self ):
         self.__run_cat_workflow( inputs_by='step_uuid' )
 
+    @skip_without_tool( "cat1" )
+    def test_run_workflow_by_uuid_implicitly( self ):
+        self.__run_cat_workflow( inputs_by='uuid_implicitly' )
+
     @skip_without_tool( "cat1" )
     def test_run_workflow_by_name( self ):
         self.__run_cat_workflow( inputs_by='name' )