Outline tracking alternative scatter types.

Keeping this WIP for now since I guess it isn't needed for the GA4GH challenge.

lib/galaxy/managers/workflows.py

@@ -880,6 +880,7 @@ def __module_from_dict( self, trans, steps, steps_by_external_id, step_dict, **k
                 step_input = model.WorkflowStepInput()
                 step_input.name = input_dict["name"]
                 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)
                 step.inputs.append(step_input)
 
         # Create the model class for the step

lib/galaxy/model/__init__.py

@@ -3953,12 +3953,14 @@ def log_str(self):
 class WorkflowStepInput( object ):
 
     default_merge_type = "merge_flattened"
+    default_scatter_type = "dotproduct"
 
     def __init__( self ):
         self.id = None
         self.name = None
         self.default_value = None
         self.merge_type = self.default_merge_type
+        self.scatter_type = self.default_scatter_type
 
 
 class WorkflowStepConnection( object ):

lib/galaxy/model/mapping.py

@@ -848,6 +848,7 @@
     Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ),
     Column( "name", Unicode( 255 ) ),
     Column( "merge_type", TEXT ),
+    Column( "scatter_type", TEXT ),
     Column( "default_value", JSONType ) )
 
 

lib/galaxy/model/migrate/versions/0137_worklfow_step_input_definitions.py

@@ -19,6 +19,7 @@
     Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ),
     Column( "name", Unicode( 255 ) ),
     Column( "merge_type", TEXT ),
+    Column( "scatter_type", TEXT ),
     Column( "default_value", JSONType ),
 )
 

lib/galaxy/tools/cwl/parser.py

@@ -745,6 +745,7 @@ def to_dict(self):
         }
         if "linkMerge" in self._cwl_input:
             as_dict["merge_type"] = self._cwl_input["linkMerge"]
+        as_dict["scatter_method"] = self.step_proxy._step.tool["scatterMethod"]
         return as_dict
 
 

lib/galaxy/workflow/modules.py

@@ -985,6 +985,12 @@ def _find_collections_to_match( self, tool, progress, step ):
         collections_to_match = matching.CollectionsToMatch()
 
         def callback( input, prefixed_name, **kwargs ):
+            step_input = step.inputs_by_name[ prefixed_name ]
+            scatter_type = "dotproduct"
+            if step_input:
+                scatter_type = step_input.scatter_type
+            assert scatter_type == "dotproduct"
+
             is_data_param = isinstance( input, DataToolParameter )
             if is_data_param and not input.multiple:
                 data = progress.replacement_for_tool_input( step, input, prefixed_name )