Merge pull request galaxyproject#8643 from mvdbeek/py3_xml_fixes

[19.09] Fix issue with xml comment handling on python 3

Author: jmchilton

lib/galaxy/util/tool_shed/xml_util.py

@@ -11,16 +11,25 @@
 log = logging.getLogger(__name__)
 
 
-class Py27CommentedTreeBuilder(XmlET.TreeBuilder):
+class CommentedTreeBuilder(XmlET.TreeBuilder):
+
+    non_comment_seen = False
 
     def doctype(*args):
         # handle deprecation warning for XMLParsing a file with DOCTYPE
         pass
 
+    def start(self, tag, attrib):
+        if tag is not XmlET.Comment:
+            self.non_comment_seen = True
+        super(CommentedTreeBuilder, self).start(tag, attrib)
+
     def comment(self, data):
-        self.start(XmlET.Comment, {})
-        self.data(data)
-        self.end(XmlET.Comment)
+        if self.non_comment_seen:
+            # Cannot start XML file with comment
+            self.start(XmlET.Comment, {})
+            self.data(data)
+            self.end(XmlET.Comment)
 
 
 def create_and_write_tmp_file(elem):
@@ -84,7 +93,7 @@ def parse_xml(file_name, check_exists=True):
 
     with open(file_name, 'r') as fobj:
         try:
-            tree = XmlET.parse(fobj, parser=XmlET.XMLParser(target=Py27CommentedTreeBuilder()))
+            tree = XmlET.parse(fobj, parser=XmlET.XMLParser(target=CommentedTreeBuilder()))
         except Exception as e:
             error_message = "Exception attempting to parse %s: %s" % (str(file_name), str(e))
             log.exception(error_message)

lib/tool_shed/galaxy_install/tools/data_manager.py

@@ -131,6 +131,8 @@ def install_data_managers(self, shed_data_manager_conf_filename, metadata_dict,
                                                                       tool_path=shed_config_dict.get('tool_path', ''))
                     if data_manager:
                         rval.append(data_manager)
+                elif elem.tag is ElementTree.Comment:
+                    pass
                 else:
                     log.warning("Encountered unexpected element '%s':\n%s" % (elem.tag, xml_to_string(elem)))
                 config_elems.append(elem)