1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d61de8f36292/ Changeset: d61de8f36292 User: Dave Bouvier Date: 2013-11-12 22:08:56 Summary: Clean up commit 11300:04663654f82d. Affected #: 2 files diff -r 9f04c4d80165d1f5261caf736aa11dbd86e36de3 -r d61de8f362929483c2a6a6cb8e7b7be77fa5cfa4 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -108,7 +108,6 @@ if proprietary_converter_path or proprietary_display_path and not handling_proprietary_datatypes: handling_proprietary_datatypes = True for elem in registration.findall( 'datatype' ): - self.log.debug( elem.attrib ) extension = elem.get( 'extension', None ) dtype = elem.get( 'type', None ) type_extension = elem.get( 'type_extension', None ) @@ -161,7 +160,6 @@ ok = False if ok: datatype_class = None - self.log.debug( [ proprietary_path, proprietary_datatype_module, datatype_class_name ] ) if proprietary_path and proprietary_datatype_module and datatype_class_name: # We need to change the value of sys.path, so do it in a way that is thread-safe. lock = threading.Lock() @@ -183,7 +181,6 @@ try: # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution. fields = datatype_module.split( '.' ) - self.log.debug( fields ) module = __import__( fields.pop(0) ) for mod in fields: module = getattr( module, mod ) @@ -196,7 +193,6 @@ # A new tool shed repository that contains proprietary datatypes is being installed, and since installation # is occurring after the datatypes registry has been initialized, its contents cannot be overridden by new # introduced conflicting data types. - self.log.warning( "Ignoring conflicting datatype with extension '%s' from %s." % ( extension, config ) ) if make_subclass: datatype_class = type( datatype_class_name, ( datatype_class, ), {} ) if extension in self.datatypes_by_extension: @@ -243,6 +239,8 @@ else: if elem not in self.display_app_containers: self.display_app_containers.append( elem ) + elif ( extension and ( dtype or type_extension ) ) and ( extension in self.datatypes_by_extension and not override ): + self.log.warning( "Ignoring conflicting datatype with extension '%s' from %s." % ( extension, config ) ) # Load datatype sniffers from the config self.load_datatype_sniffers( root, deactivate=deactivate, diff -r 9f04c4d80165d1f5261caf736aa11dbd86e36de3 -r d61de8f362929483c2a6a6cb8e7b7be77fa5cfa4 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -54,7 +54,7 @@ common_install_util.activate_repository( trans, repository ) except Exception, e: error_message = "Error activating repository %s: %s" % ( repository.name, str( e ) ) - log.debug( error_message ) + log.exception( error_message ) message = '%s.<br/>You may be able to resolve this by uninstalling and then reinstalling the repository. Click <a href="%s">here</a> to uninstall the repository.' \ % ( error_message, web.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) ) ) status = 'error' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.