Bugfix: Yet another bug fix for workflow extraction with collection operations.

Fail, fail, fail.

lib/galaxy/model/__init__.py

@@ -2864,6 +2864,13 @@ class DatasetCollectionElement( object, Dictifiable ):
     def dataset( self ):
         return self.dataset_instance.dataset
 
+    def first_dataset_instance( self ):
+        element_object = self.element_object
+        if isinstance( element_object, DatasetCollection ):
+            return element_object.dataset_instances[ 0 ]
+        else:
+            return element_object
+
     def copy_to_collection( self, collection ):
         new_element = DatasetCollectionElement(
             element=self.element_object,

lib/galaxy/workflow/extract.py

@@ -293,6 +293,8 @@ def __cleanup_param_values( inputs, values ):
                 # HACK: Nested associations are not yet working, but we
                 #       still need to clean them up so we can serialize
                 # if not( prefix ):
+                if isinstance( tmp, model.DatasetCollectionElement ):
+                    tmp = tmp.first_dataset_instance()
                 if tmp:  # this is false for a non-set optional dataset
                     if not isinstance(tmp, list):
                         associations.append( ( tmp.hid, prefix + key ) )