comparison data_manager/add_ctat_resource_lib.py @ 46:f4f48007db67 draft

Uploaded

45:3acb7bc809b5

    # But I do not get input values from the json file, but rather from command line.
    # Just leaving the following code as a comment, in case it might be useful to someone later.
    # params = from_json_string(open(filename).read())
    # target_directory = params['output_data'][0]['extra_files_path']
    # os.mkdir(target_directory)

    print "The value of download_url argument is:\n\t{:s}".format(str(args.download_url))
    sys.stdout.flush()
    
    lib_was_built = False
    extracted_directory = None
    source_data_directory = None
    genome_build_directory = None
    download_url_is_set = (args.download_url is not None) and (args.download_url != "")
    download_location_is_set = (args.download_location is not None) and (args.download_location != "")
    source_location_is_set = (args.source_location is not None) and (args.source_location != "")
    build_location_is_set = (args.build_location is not None) and (args.build_location != "")
    # FIX - need to make sure we are handling all "possible" combinations of arguments.
    # Probably would be good if we could simplify/remove some of them.
    # But I think the current interface is using them all.

    if download_url_is_set:
        if source_location_is_set:
            raise ValueError("Argument --source_location cannot be used in combination with --download_url.")
        if not download_location_is_set:
            raise ValueError("Argument --download_url requires that --download_location be specified.")
        downloaded_filename_full_path = \

46:f4f48007db67

    # But I do not get input values from the json file, but rather from command line.
    # Just leaving the following code as a comment, in case it might be useful to someone later.
    # params = from_json_string(open(filename).read())
    # target_directory = params['output_data'][0]['extra_files_path']
    # os.mkdir(target_directory)
    
    lib_was_built = False
    extracted_directory = None
    source_data_directory = None
    genome_build_directory = None
    download_url_is_set = (args.download_url is not None) and (args.download_url != "")
    download_location_is_set = (args.download_location is not None) and (args.download_location != "")
    source_location_is_set = (args.source_location is not None) and (args.source_location != "")
    build_location_is_set = (args.build_location is not None) and (args.build_location != "")
    
    if download_url_is_set:
        print "The value of download_url argument is:\n\t{:s}".format(str(args.download_url))
        sys.stdout.flush()
        if source_location_is_set:
            raise ValueError("Argument --source_location cannot be used in combination with --download_url.")
        if not download_location_is_set:
            raise ValueError("Argument --download_url requires that --download_location be specified.")
        downloaded_filename_full_path = \