Write out datatype registry when loading set_metadata tool

lib/galaxy/app.py

@@ -123,7 +123,6 @@ def __init__( self, **kwargs ):
         # Load datatype converters defined in local datatypes_conf.xml
         self.datatypes_registry.load_datatype_converters( self.toolbox )
         # Load external metadata tool
-        self.datatypes_registry.to_xml_file()
         self.datatypes_registry.load_external_metadata_tool( self.toolbox )
         # Load history import/export tools.
         load_lib_tools( self.toolbox )

lib/galaxy/datatypes/registry.py

@@ -663,6 +663,7 @@ def load_external_metadata_tool( self, toolbox ):
         # We need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated
         # tool.  We'll load a special tool to be used for Auto-Detecting metadata; this is less than ideal, but effective
         # Properly building a tool without relying on parsing an XML file is near difficult...so we bundle with Galaxy.
+        self.to_xml_file()
         set_meta_tool = toolbox.load_hidden_lib_tool( "galaxy/datatypes/set_metadata_tool.xml" )
         self.set_external_metadata_tool = set_meta_tool
         self.log.debug( "Loaded external metadata tool: %s", self.set_external_metadata_tool.id )
@@ -856,7 +857,6 @@ def edam_data( self ):
     def integrated_datatypes_configs( self ):
         if self.xml_filename and os.path.isfile( self.xml_filename ):
             return self.xml_filename
-        self.to_xml_file()
         return self.xml_filename
 
     def to_xml_file( self ):

lib/galaxy/queue_worker.py

@@ -110,8 +110,8 @@ def _get_new_toolbox(app):
     new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)
     new_toolbox.data_manager_tools = app.toolbox.data_manager_tools
     app.datatypes_registry.load_datatype_converters(new_toolbox, use_cached=True)
+    app.datatypes_registry.load_external_metadata_tool(new_toolbox)
     load_lib_tools(new_toolbox)
-    new_toolbox.load_hidden_lib_tool( "galaxy/datatypes/set_metadata_tool.xml" )
     [new_toolbox.register_tool(tool) for tool in new_toolbox.data_manager_tools.values()]
     app.toolbox = new_toolbox
     send_local_control_task(app, 'rebuild_toolbox_search_index')

lib/galaxy/tools/parser/xml.py

@@ -594,7 +594,7 @@ def __parse_param_elem( param_elem, i=0 ):
     else:
         value = None
     attrib['children'] = param_elem
-    if attrib['children']:
+    if attrib['children'] is not None:
         # At this time, we can assume having children only
         # occurs on DataToolParameter test items but this could
         # change and would cause the below parsing to change

lib/tool_shed/galaxy_install/installed_repository_manager.py

@@ -129,7 +129,6 @@ def activate_repository( self, repository ):
                 display_path = installed_repository_dict.get( 'display_path' )
                 if display_path is not None:
                     cdl.load_installed_display_applications( installed_repository_dict, deactivate=False )
-                self.app.datatypes_registry.to_xml_file()
 
     def add_entry_to_installed_repository_dependencies_of_installed_repositories( self, repository ):
         """
@@ -740,7 +739,6 @@ def load_proprietary_datatypes( self ):
                 installed_repository_dict = cdl.load_installed_datatypes( tool_shed_repository, relative_install_dir )
                 if installed_repository_dict:
                     self.installed_repository_dicts.append( installed_repository_dict )
-        self.app.datatypes_registry.to_xml_file()
 
     def load_proprietary_converters_and_display_applications( self, deactivate=False ):
         cdl = custom_datatype_manager.CustomDatatypeLoader( self.app )