Merge branch 'release_16.01' into release_16.04

Conflicts:
	lib/galaxy/util/__init__.py

lib/galaxy/tools/toolbox/integrated_panel.py

@@ -3,6 +3,7 @@ import shutil
 import tempfile
 import time
 import traceback
+from xml.sax.saxutils import escape
 
 from .panel import ToolPanelElements
 from .panel import panel_item_types
@@ -78,7 +79,7 @@ class ManagesIntegratedToolPanelMixin:
                     section_id = item.id or ''
                     section_name = item.name or ''
                     section_version = item.version or ''
-                    os.write( fd, '    <section id="%s" name="%s" version="%s">\n' % ( section_id, section_name, section_version ) )
+                    os.write( fd, '    <section id="%s" name="%s" version="%s">\n' % ( escape(section_id), escape(section_name), section_version ) )
                     for section_key, section_item_type, section_item in item.panel_items_iter():
                         if section_item_type == panel_item_types.TOOL:
                             if section_item:

lib/galaxy/util/__init__.py

@@ -26,6 +26,7 @@ from datetime import datetime
 from hashlib import md5
 from os.path import normpath, relpath
 from xml.etree import ElementInclude, ElementTree
+from xml.etree.ElementTree import ParseError
 
 from six import binary_type, iteritems, PY3, string_types, text_type
 from six.moves import email_mime_text, xrange, zip
@@ -40,6 +41,7 @@ except ImportError:
     docutils_html4css1 = None
 
 from .inflection import English, Inflector
+
 inflector = Inflector(English)
 
 if PY3:
@@ -177,7 +179,11 @@ def parse_xml( fname ):
         def doctype( *args ):
             pass
     tree = ElementTree.ElementTree()
-    root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) )
+    try:
+        root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) )
+    except ParseError:
+        log.exception("Error parsing file %s", fname)
+        raise
     ElementInclude.include( root )
     return tree