Exemple #1
0
def list_libraries(context,galaxy,path,long_listing):
    """
    List data libraries and contents.

    Prints details of the data library and folders
    specified by PATH, in GALAXY instance.

    PATH should be of the form
    'data_library[/folder[/subfolder[...]]]'
    """
    # Get a Galaxy instance
    gi = context.galaxy_instance(galaxy)
    if gi is None:
        logger.critical("Failed to connect to Galaxy instance")
        return 1
    # List folders in data library
    if path:
        libraries.list_library_contents(gi,path,
                                        long_listing_format=
                                        long_listing)
    else:
        libraries.list_data_libraries(gi)
Exemple #2
0
def manage_libraries(args=None):
    """
    Implements the 'manage_libraries' utility

    """
    deprecation_warning()
    if args is None:
        args = sys.argv[1:]

    p = base_parser(usage=\
                    "\n\t%prog list GALAXY_URL [options]"
                    "\n\t%prog create_library GALAXY_URL [options] NAME"
                    "\n\t%prog create_folder GALAXY_URL [options] PATH"
                    "\n\t%prog add_datasets GALAXY_URL [options] DEST FILE...",
                    description="Manage and populate data libraries in a "
                    "Galaxy instance")
    
    commands = ['list','create_library','create_folder','add_datasets']

    # Get compulsory arguments
    if len(args) == 1:
        if args[0] == '-h' or args[0] == '--help':
            p.print_usage()
        elif args[0] == '--version':
            p.print_version()
        sys.exit(0)
    if len(args) < 2:
        p.error("need to supply a command and a Galaxy URL/alias")
    command = args[0]
    galaxy_url = args[1]

    # Setup additional command line options
    if command not in commands:
        p.error("unrecognised command: '%s'" % command)
    elif command == 'list':
        p.set_usage("%prog list GALAXY_URL [options]")
        p.add_option('-l',action='store_true',
                     dest='long_listing_format',default=False,
                     help="use a long listing format (include ids, "
                     "descriptions and file sizes and paths)")
    elif command == 'create_library':
        p.set_usage("%prog create_library GALAXY_URL [options] NAME")
        p.add_option('-d','--description',action='store',
                     dest='description',default=None,
                     help="optional description")
        p.add_option('-s','--synopsis',action='store',dest='synopsis',
                     default=None,help="optional synopsis")
    elif command == 'create_folder':
        p.set_usage("%prog create_folder GALAXY_URL [options] PATH")
        p.add_option('-d','--description',action='store',
                     dest='description',default=None,
                     help="optional description")
    elif command == 'add_datasets':
        p.set_usage("%prog add_datasets GALAXY_URL [options] DEST FILE...")
        p.add_option('--server',action='store_true',dest='from_server',
                     default=False,
                     help="upload files from Galaxy server file system "
                     "paths (default is to upload files from local "
                     "system)")
        p.add_option('--link',action='store_true',dest='link',
                     default=False,
                     help="create symlinks to files on server (only "
                     "valid if used with --server; default is to copy "
                     "files into Galaxy)")
        p.add_option('--dbkey',action='store',dest='dbkey',default='?',
                     help="dbkey to assign to files (default is '?')")
        p.add_option('--file_type',action='store',dest='file_type',
                     default='auto',
                     help="file type to assign to files (default is "
                     "'auto')")

    # Process remaining arguments on command line
    if args[1] in ('-h','--help','--version'):
        args = args[1:]
    else:
        args = args[2:]
    options,args = p.parse_args(args)
    handle_debug(debug=options.debug)
    handle_suppress_warnings(suppress_warnings=options.suppress_warnings)
    handle_ssl_warnings(verify=(not options.no_verify))

    # Handle password if required
    email,password = handle_credentials(options.username,
                                        options.galaxy_password,
                                        prompt="Password for %s: " % galaxy_url)

    # Get a Galaxy instance
    gi = get_galaxy_instance(galaxy_url,api_key=options.api_key,
                             email=email,password=password,
                             verify_ssl=(not options.no_verify))
    if gi is None:
        logger.critical("Failed to connect to Galaxy instance")
        sys.exit(1)

    # Execute command
    if command == 'list':
        if len(args) == 1:
            # List folders in data library
            libraries.list_library_contents(gi,args[0],long_listing_format=
                                            options.long_listing_format)
        else:
            # List data libraries
            libraries.list_data_libraries(gi)
    elif command == 'create_library':
        # Create a new data library
        if len(args) == 1:
            libraries.create_library(gi,args[0],
                                     description=options.description,
                                     synopsis=options.synopsis)
        else:
            p.error("Usage: create_library NAME")
    elif command == 'create_folder':
        # Create a new folder data library
        if len(args) == 1:
            libraries.create_folder(gi,args[0],
                                    description=options.description)
        else:
            p.error("Usage: create_folder PATH")
    elif command == 'add_datasets':
        # Add a dataset to a library
        if len(args) < 2:
            p.error("Usage: add_datasets DEST FILE [FILE...]")
        libraries.add_library_datasets(gi,args[0],args[1:],
                                       from_server=options.from_server,
                                       link_only=options.link,
                                       file_type=options.file_type,
                                       dbkey=options.dbkey)