1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/337e5b6bd7dc/ changeset: 337e5b6bd7dc branch: stable user: greg date: 2013-02-18 17:04:29 summary: Fix for handling proprietary datatyps definitions in repositories being installed from the tool shed when only datatyes that subclass from those in the Galaxy frameowrk are defined (i.e., there are no proprietary datatype class files for the datatypes). In addition, this changeset now properly handles installing a tool shed repository that included prioretary datatype definitions (they were failing due to a bug in this same method). affected #: 1 file
diff -r 8cd0793b0fc65b57f8fd93cfffc19ba105d190cf -r 337e5b6bd7dc5696087c436e54192149c1bc8bc3 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -120,12 +120,24 @@ be False when a tool shed repository is being installed. Since installation is occurring after the datatypes registry has been initialized, the registry's contents cannot be overridden by conflicting data types. """ - tree = util.parse_xml( datatypes_config ) + try: + tree = util.parse_xml( datatypes_config ) + except Exception, e: + log.debug( "Error parsing %s, exception: %s" % ( datatypes_config, str( e ) ) ) + return None, None datatypes_config_root = tree.getroot() - # Path to datatype converters - converter_path = None - # Path to datatype display applications - display_path = None + registration = datatypes_config_root.find( 'registration' ) + if registration is None: + # We have valid XML, but not a valid proprietary datatypes definition. + return None, None + sniffers = datatypes_config_root.find( 'sniffers' ) + converter_path, display_path = get_converter_and_display_paths( registration, relative_install_dir ) + if converter_path: + # Path to datatype converters + registration.attrib[ 'proprietary_converter_path' ] = converter_path + if display_path: + # Path to datatype display applications + registration.attrib[ 'proprietary_display_path' ] = display_path relative_path_to_datatype_file_name = None datatype_files = datatypes_config_root.find( 'datatype_files' ) datatype_class_modules = [] @@ -148,12 +160,6 @@ break break if datatype_class_modules: - registration = datatypes_config_root.find( 'registration' ) - converter_path, display_path = get_converter_and_display_paths( registration, relative_install_dir ) - if converter_path: - registration.attrib[ 'proprietary_converter_path' ] = converter_path - if display_path: - registration.attrib[ 'proprietary_display_path' ] = display_path for relative_path_to_datatype_file_name in datatype_class_modules: datatype_file_name_path, datatype_file_name = os.path.split( relative_path_to_datatype_file_name ) for elem in registration.findall( 'datatype' ): @@ -170,20 +176,16 @@ # The value of proprietary_path must be an absolute path due to job_working_directory. elem.attrib[ 'proprietary_path' ] = os.path.abspath( datatype_file_name_path ) elem.attrib[ 'proprietary_datatype_module' ] = proprietary_datatype_module - sniffers = datatypes_config_root.find( 'sniffers' ) - else: - sniffers = None - fd, proprietary_datatypes_config = tempfile.mkstemp() - os.write( fd, '<?xml version="1.0"?>\n' ) - os.write( fd, '<datatypes>\n' ) - os.write( fd, '%s' % util.xml_to_string( registration ) ) - if sniffers: - os.write( fd, '%s' % util.xml_to_string( sniffers ) ) - os.write( fd, '</datatypes>\n' ) - os.close( fd ) - os.chmod( proprietary_datatypes_config, 0644 ) - else: - proprietary_datatypes_config = datatypes_config + # Temporarily persist the proprietary datatypes configuration file so it can be loaded into the datatypes registry. + fd, proprietary_datatypes_config = tempfile.mkstemp() + os.write( fd, '<?xml version="1.0"?>\n' ) + os.write( fd, '<datatypes>\n' ) + os.write( fd, '%s' % util.xml_to_string( registration ) ) + if sniffers: + os.write( fd, '%s' % util.xml_to_string( sniffers ) ) + os.write( fd, '</datatypes>\n' ) + os.close( fd ) + os.chmod( proprietary_datatypes_config, 0644 ) # Load proprietary datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=proprietary_datatypes_config, deactivate=deactivate, override=override ) if datatype_files:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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