diff --git a/lib/galaxy/web/controllers/library_common.py b/lib/galaxy/web/controllers/library_common.py
index fd500070ec8..1b23efec016 100644
--- a/lib/galaxy/web/controllers/library_common.py
+++ b/lib/galaxy/web/controllers/library_common.py
@@ -911,7 +911,7 @@ class LibraryCommon( BaseController ):
                 dataset_names = []
                 created_ldda_ids = ''
                 for hda_id in hda_ids:
-                    hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( hda_id ) )
+                    hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( hda_id )
                     if hda:
                         ldda = hda.to_library_dataset_dataset_association( target_folder=folder, replace_dataset=replace_dataset )
                         created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( ldda.id ) )
diff --git a/lib/galaxy/web/controllers/requests.py b/lib/galaxy/web/controllers/requests.py
index 2879ddf67f9..2efeda2bde4 100644
--- a/lib/galaxy/web/controllers/requests.py
+++ b/lib/galaxy/web/controllers/requests.py
@@ -608,7 +608,7 @@ class Requests( BaseController ):
         actions_to_check = [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ]
         libraries = odict()
         for library in all_libraries:
-            can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check )
+            can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( trans.user, roles, library, actions_to_check )
             if can_show:
                 libraries[ library ] = hidden_folder_ids
         # create data library selectbox with refresh on change enabled
@@ -661,7 +661,8 @@ class Requests( BaseController ):
             else:
                 folder_list.add_option('Select one', 'none')
             # get all show-able folders for the selected library
-            showable_folders = trans.app.security_agent.get_showable_folders( user, roles, 
+            showable_folders = trans.app.security_agent.get_showable_folders( trans.user,
+                                                                              roles, 
                                                                               selected_lib, 
                                                                               actions_to_check, 
                                                                               selected_hidden_folder_ids )
diff --git a/templates/library/common/common.mako b/templates/library/common/common.mako
index 19a69e1ac27..b165d4e9ec4 100644
--- a/templates/library/common/common.mako
+++ b/templates/library/common/common.mako
@@ -80,7 +80,7 @@
                     %if replace_dataset not in [ None, 'None' ]:
                         <input type="hidden" name="replace_id" value="${trans.security.encode_id( replace_dataset.id )}"/>
                         <div class="form-row">
-                            You are currently selecting a new file to replace '<a href="${h.url_for( controller=cntrller, action='ldda_display_info', library_id=library_id, folder_id=folder_id, id=trans.security.encode_id( replace_dataset.library_dataset_dataset_association.id ) )}">${replace_dataset.name}</a>'.
+                            You are currently selecting a new file to replace '<a href="${h.url_for( controller='library_common', action='ldda_display_info', cntrller=cntrller, library_id=library_id, folder_id=folder_id, id=trans.security.encode_id( replace_dataset.library_dataset_dataset_association.id ) )}">${replace_dataset.name}</a>'.
                             <div style="clear: both"></div>
                         </div>
                     %endif
@@ -302,7 +302,7 @@
                         %if replace_dataset not in [ None, 'None' ]:
                             <input type="hidden" name="replace_id" value="${trans.security.encode_id( replace_dataset.id )}"/>
                             <div class="form-row">
-                                You are currently selecting a new file to replace '<a href="${h.url_for( controller=cntrller, action='ldda_display_info', library_id=library_id, folder_id=folder_id, id=trans.security.encode_id( replace_dataset.library_dataset_dataset_association.id ) )}">${replace_dataset.name}</a>'.
+                                You are currently selecting a new file to replace '<a href="${h.url_for( controller='library_common', action='ldda_display_info', cntrller=cntrller, library_id=library_id, folder_id=folder_id, id=trans.security.encode_id( replace_dataset.library_dataset_dataset_association.id ) )}">${replace_dataset.name}</a>'.
                                 <div style="clear: both"></div>
                             </div>
                         %endif
diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py
index 3f550a4ea1b..b66c0ee5300 100644
--- a/test/functional/test_toolbox.py
+++ b/test/functional/test_toolbox.py
@@ -60,10 +60,18 @@ class ToolTestCase( TwillTestCase ):
             page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[i], all_inputs)
             self.submit_form( **page_inputs )
             print "page_inputs (%i)" % i, page_inputs
-        # Check the results ( handles single or multiple tool outputs )
+        # Check the results ( handles single or multiple tool outputs ).  Make sure to pass the correct hid.
+        # The output datasets from the tool should be in the same order as the testdef.outputs.
+        data_list = self.get_history_as_data_list()
+        self.assertTrue( data_list )
+        elem_index = 0 - len( testdef.outputs )
         for output_tuple in testdef.outputs:
             name, file, sort = output_tuple
-            self.verify_dataset_correctness( file, maxseconds=testdef.maxseconds, sort=sort )
+            # Get the correct hid
+            elem = data_list[ elem_index ]
+            elem_hid = elem.get( 'hid' )
+            elem_index += 1
+            self.verify_dataset_correctness( file, hid=elem_hid, maxseconds=testdef.maxseconds, sort=sort )
         self.delete_history( id=self.security.encode_id( latest_history.id ) )
 
     def __expand_grouping( self, tool_inputs, declared_inputs, prefix='' ):