Merge pull request #4389 from jmchilton/output_collect_refactor

Refactor ToolOutputCollectionStructure...
galaxyproject · Aug 8, 2017 · d53a542 · d53a542
2 parents d2394aa + e811221
commit d53a542
Showing 1 changed file with 12 additions and 8 deletions.
diff --git a/lib/galaxy/tools/parser/output_objects.py b/lib/galaxy/tools/parser/output_objects.py
@@ -118,11 +118,7 @@ def known_outputs( self, inputs, type_registry ):
         if len( self.outputs ) > 1:
             output_parts = [ToolOutputCollectionPart(self, k, v) for k, v in self.outputs.items()]
         else:
-            # either must have specified structured_like or something worse
-            if self.structure.structured_like:
-                collection_prototype = inputs[ self.structure.structured_like ].collection
-            else:
-                collection_prototype = type_registry.prototype( self.structure.collection_type )
+            collection_prototype = self.structure.collection_prototype( inputs, type_registry )
 
             def prototype_dataset_element_to_output( element, parent_ids=[] ):
                 name = element.element_identifier
@@ -178,9 +174,9 @@ class ToolOutputCollectionStructure( object ):
     def __init__(
         self,
         collection_type,
-        collection_type_source,
-        structured_like,
-        dataset_collector_descriptions,
+        collection_type_source=None,
+        structured_like=None,
+        dataset_collector_descriptions=None,
     ):
         self.collection_type = collection_type
         self.collection_type_source = collection_type_source
@@ -194,6 +190,14 @@ def __init__(
             raise ValueError( "Cannot specify dynamic structure (discovered_datasets) and structured_like attribute." )
         self.dynamic = dataset_collector_descriptions is not None
 
+    def collection_prototype( self, inputs, type_registry ):
+        # either must have specified structured_like or something worse
+        if self.structured_like:
+            collection_prototype = inputs[ self.structured_like ].collection
+        else:
+            collection_prototype = type_registry.prototype( self.collection_type )
+        return collection_prototype
+
 
 class ToolOutputCollectionPart( object ):