comparison directory_copier.py @ 1:1487421505f1 draft

Uploaded correct tool this time

0:25b07ce180d4

def report_error(*args):
    sys.stderr.write(' '.join(map(str,args)) + '\n')
    sys.stderr.flush()
    sys.exit(1)


def get_tool_data(name):
    root_dir = os.path.dirname((os.path.realpath(__file__)))
    path = os.path.join(root_dir,"tool-data",name)
    if not(os.path.isfile(path)): 
        report_error(name,"file not found in tool's tool-data folder. Please ask you galaxy admin to add it back")
    return path


def check_white_list(path_to_check):
    white_list = get_tool_data("white-list.ini")
    with open(white_list, 'r') as white_list_file:
        for line in white_list_file:
            line = line.strip()
            if len(line) >= 1 and path_to_check.startswith(line):
                return True
    report_error(path_to_check,"has not been included in the white list. Please contact the local galaxy admin to add it.")


def check_black_list(path_to_check):
    black_list = get_tool_data("black-list.ini")
    with open(black_list, 'r') as black_list_file:
        for line in black_list_file:
            line = line.strip()
            if len(line) >= 1 and line in path_to_check:
                report_error(line,"has been black list so",path_to_check,"is not allowed. Please contact the local galaxy admin to change that, or add a symlink.")
    return True


def check_pattern_get_new_name(a_file, ending, options):
    if options.start:
        if not(a_file.startswith(options.start)):

    path = options.path.strip()
    if path[-1] != '/':
        path = path + "/"
    check_white_list(path)
    print path, "white listed"
    check_black_list(path)
    print path, "not black listed"
    copy_and_link(path, options)

1:1487421505f1

def report_error(*args):
    sys.stderr.write(' '.join(map(str,args)) + '\n')
    sys.stderr.flush()
    sys.exit(1)


def check_pattern_get_new_name(a_file, ending, options):
    if options.start:
        if not(a_file.startswith(options.start)):

    path = options.path.strip()
    if path[-1] != '/':
        path = path + "/"
    copy_and_link(path, options)