Remove operations from custom_datatype_manager

Updating the upload file formats is handled when loading the datatype
into the registry, and reloading the upload tool seems unnecessary and
insufficient, since this would only affect the current web handler. In
any case removed and added datatypes are immediately propagated to the
upload tool.

lib/galaxy/tools/__init__.py

@@ -34,7 +34,6 @@
 from galaxy.tools.actions.data_manager import DataManagerToolAction
 from galaxy.tools.actions.data_source import DataSourceToolAction
 from galaxy.tools.actions.model_operations import ModelOperationToolAction
-from galaxy.tools.actions.upload import UploadToolAction
 from galaxy.tools.deps import (
     CachedDependencyManager,
     views
@@ -249,13 +248,6 @@ def create_tool( self, config_file, repository_id=None, guid=None, **kwds ):
         tool = ToolClass( config_file, tool_source, self.app, guid=guid, repository_id=repository_id, **kwds )
         return tool
 
-    def handle_datatypes_changed( self ):
-        """ Refresh upload tools when new datatypes are added. """
-        for tool_id in self._tools_by_id:
-            tool = self._tools_by_id[ tool_id ]
-            if isinstance( tool.tool_action, UploadToolAction ):
-                self.reload_tool_by_id( tool_id )
-
     def get_tool_components( self, tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=False ):
         """
         Retrieve all loaded versions of a tool from the toolbox and return a select list enabling

lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py

@@ -1,9 +1,8 @@
 import logging
 import os
 
-from galaxy.util import asbool
 from tool_shed.util import basic_util, hg_util, shed_util_common as suc
-from tool_shed.util import tool_util, xml_util
+from tool_shed.util import xml_util
 
 log = logging.getLogger( __name__ )
 
@@ -84,25 +83,8 @@ def alter_config_and_load_prorietary_datatypes( self, datatypes_config, relative
                                                     config=datatypes_config_root,
                                                     deactivate=deactivate,
                                                     override=override )
-        if deactivate:
-            # Reload the upload tool to eliminate deactivated datatype extensions from the file_type
-            # select list.
-            tool_util.reload_upload_tools( self.app )
-        else:
-            self.append_to_datatypes_registry_upload_file_formats( registration )
-            tool_util.reload_upload_tools( self.app )
         return converter_path, display_path
 
-    def append_to_datatypes_registry_upload_file_formats( self, elem ):
-        # See if we have any datatypes that should be displayed in the upload tool's file_type select list.
-        for datatype_elem in elem.findall( 'datatype' ):
-            extension = datatype_elem.get( 'extension', None )
-            display_in_upload = datatype_elem.get( 'display_in_upload', None )
-            if extension is not None and display_in_upload is not None:
-                display_in_upload = asbool( str( display_in_upload ) )
-                if display_in_upload and extension not in self.app.datatypes_registry.upload_file_formats:
-                    self.app.datatypes_registry.upload_file_formats.append( extension )
-
     def create_repository_dict_for_proprietary_datatypes( self, tool_shed, name, owner, installed_changeset_revision,
                                                           tool_dicts, converter_path=None, display_path=None ):
         return dict( tool_shed=tool_shed,

lib/tool_shed/util/tool_util.py

@@ -272,8 +272,3 @@ def panel_entry_per_tool( tool_section_dict ):
         if k not in [ 'id', 'version', 'name' ]:
             return True
     return False
-
-
-def reload_upload_tools( app ):
-    if hasattr( app, 'toolbox' ):
-        app.toolbox.handle_datatypes_changed()