Update the integrated_toon_conf.xml file only if a new config setting is True. This keeps things that start up the app (like functional tests) from updating the file.

lib/galaxy/config.py

@@ -70,6 +70,7 @@ class Configuration( object ):
                 self.hours_between_check = 12
         except:
             self.hours_between_check = 12
+        self.update_integrated_tool_panel = kwargs.get( "update_integrated_tool_panel", True )
         self.tool_secret = kwargs.get( "tool_secret", "" )
         self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
         self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) )

lib/galaxy/tools/__init__.py

@@ -75,10 +75,12 @@ class ToolBox( object ):
         if self.integrated_tool_panel_config_has_contents:
             # Load self.tool_panel based on the order in self.integrated_tool_panel.
             self.load_tool_panel()
-        # Always write the current in-memory integrated_tool_panel to the integrated_tool_panel.xml file.
-        # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel
-        # config files, adding or removing locally developed tools or workflows.
-        self.write_integrated_tool_panel_config_file()
+        if app.config.update_integrated_tool_panel:
+            # Write the current in-memory integrated_tool_panel to the integrated_tool_panel.xml file.
+            # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel
+            # config files, adding or removing locally developed tools or workflows.  The value of integrated_tool_panel
+            # will be False when things like functional tests are the caller.
+            self.write_integrated_tool_panel_config_file()
     def init_tools( self, config_filename ):
         """
         Read the configuration file and load each tool.  The following tags are currently supported:

lib/galaxy/webapps/community/controllers/admin.py

@@ -430,7 +430,6 @@ class AdminController( BaseUIController, Admin ):
                 return trans.response.send_redirect( web.url_for( controller='repository',
                                                                   action='browse_repositories',
                                                                   **kwd ) )
-        # Render the list view
         return self.repository_metadata_list_grid( trans, **kwd )
     @web.expose
     @web.require_admin
@@ -504,7 +503,7 @@ class AdminController( BaseUIController, Admin ):
                 else:
                     del kwd[ 'operation' ]
             elif operation == 'delete':
-                return self.mark_repository_deleted( trans, **kwd )
+                return self.delete_repository( trans, **kwd )
             elif operation == "undelete":
                 return self.undelete_repository( trans, **kwd )
         # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change
@@ -528,12 +527,13 @@ class AdminController( BaseUIController, Admin ):
         return self.repository_list_grid( trans, **kwd )
     @web.expose
     @web.require_admin
-    def mark_repository_deleted( self, trans, **kwd ):
+    def delete_repository( self, trans, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         id = kwd.get( 'id', None )
         if id:
+            # Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. 
             ids = util.listify( id )
             count = 0
             deleted_repositories = ""
@@ -564,6 +564,7 @@ class AdminController( BaseUIController, Admin ):
         status = params.get( 'status', 'done' )
         id = kwd.get( 'id', None )
         if id:
+            # Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
             ids = util.listify( id )
             count = 0
             undeleted_repositories = ""

scripts/functional_tests.py

@@ -167,6 +167,7 @@ def main():
                                    file_path = file_path,
                                    new_file_path = new_file_path,
                                    tool_path = tool_path,
+                                   update_integrated_tool_panel = False,
                                    tool_config_file = tool_config_file,
                                    datatype_converters_config_file = "datatype_converters_conf.xml.sample",
                                    tool_parse_help = False,