Update original parse_xml function with Carl's fix. It's safe, and I know I saw that same doctype deprecation somewhere else, might as well share it.

lib/galaxy/util/__init__.py

@@ -169,11 +169,15 @@ def unique_id(KEY_SIZE=128):
     return md5(str( random.getrandbits( KEY_SIZE ) )).hexdigest()
 
 
-def parse_xml(fname):
+def parse_xml( fname ):
     """Returns a parsed xml tree"""
-    tree = ElementTree.parse(fname)
-    root = tree.getroot()
-    ElementInclude.include(root)
+    # handle deprecation warning for XMLParsing a file with DOCTYPE
+    class DoctypeSafeCallbackTarget( ElementTree.TreeBuilder ):
+        def doctype( *args ):
+            pass
+    tree = ElementTree.ElementTree()
+    root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) )
+    ElementInclude.include( root )
     return tree
 
 

lib/galaxy/visualization/registry.py

@@ -7,8 +7,6 @@ Lower level of visualization framework which does three main things:
 import os
 import shutil
 import glob
-from xml.etree import ElementTree
-from xml.etree import ElementInclude
 
 from galaxy import util
 import galaxy.model
@@ -85,16 +83,6 @@ def hasattr_recursive( item, attr_key ):
 
     return True
 
-def parse_xml( fname ):
-    # handle deprecation warning for XMLParsing a file with DOCTYPE
-    class DoctypeSafeCallbackTarget( ElementTree.TreeBuilder ):
-        def doctype( *args ):
-            pass
-    tree = ElementTree.ElementTree()
-    root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) )
-    ElementInclude.include( root )
-    return tree
-
 
 # ------------------------------------------------------------------- the registry
 class VisualizationsRegistry( pluginframework.PageServingPluginManager ):
@@ -406,7 +394,7 @@ class VisualizationsConfigParser( object ):
         Parse the given XML file for visualizations data.
         :returns: visualization config dictionary
         """
-        xml_tree = parse_xml( xml_filepath )
+        xml_tree = util.parse_xml( xml_filepath )
         visualization = self.parse_visualization( xml_tree.getroot() )
         return visualization