comparison hubArchiveCreator.py @ 2:4ced8f116509 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty

1:42337785f87b

    outputFile = args.output

    json_inputs_data = args.data_json

    inputs_data = json.loads(json_inputs_data)
    # We remove the spaces in ["name"] of inputs_data
    sanitize_name_inputs(inputs_data)

    # TODO: Check here all the binaries / tools we need. Exception if missing

    sys.exit(0)


def sanitize_name_input(string_to_sanitize):
        return string_to_sanitize \
            .replace("/", "_") \
            .replace(" ", "_")


def sanitize_name_inputs(inputs_data):
    """
    Sometimes output from Galaxy, or even just file name from user have spaces
    Also, it can contain '/' character and could break the use of os.path function
    :param inputs_data: dict[string, dict[string, string]]
    :return:
    """
    for key in inputs_data:
        inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"])


def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data):
    """
    Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
    and update the dictionary of datatype
    :param ExtensionClass: T <= Datatype
    :param array_inputs: list[string]
    :param inputs_data:
    """

    datatype_dictionary = {}

    # TODO: Optimize this double loop

            in STDOUT
        - Still access to full, brute and traceback for errors
            in STDERR
        - And further access to debug if needed
            in .log
    :return:
    """
    if not log_stdout:
        raise Exception("No log_stdout given. Stopping the application")

    # stdout for INFO / WARN / ERROR / CRITICAL
    log_stdout.setLevel(logging.INFO)

    """
    Dev Logger is defined as following:
        - Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout
        - Still access to full, brute and traceback in stderr for errors
        - And further access to debug if needed
    :return:
    """
    if not log_stdout:
        raise Exception("No log_stdout given. Stopping the application")
    log_format = '%(message)s'

    logging.getLogger().addHandler(log_stdout)

def configure_logger_stderr():
    """
    Configure what should be logged in stderr
    :return:
    """
    log_error = logging.StreamHandler(sys.stderr)
    log_error.setLevel(logging.ERROR)
    log_error_format = '%(message)s'

2:4ced8f116509

    outputFile = args.output

    json_inputs_data = args.data_json

    # TODO: Instead use a class to properly store the objects, with object_hook
    inputs_data = json.loads(json_inputs_data)
    # We remove the spaces in ["name"] of inputs_data
    sanitize_name_inputs(inputs_data)

    # TODO: Check here all the binaries / tools we need. Exception if missing

    sys.exit(0)


def sanitize_name_input(string_to_sanitize):
    """
    Sanitize the string passed in parameter by replacing '/' and ' ' by '_'

    :param string_to_sanitize:
    :return :

    :Example:

    >>> sanitize_name_input('this/is an//example')
    this_is_an__example
    """
    return string_to_sanitize \
            .replace("/", "_") \
            .replace(" ", "_")


def sanitize_name_inputs(inputs_data):
    """
    Sanitize value of the keys "name" of the dictionary passed in parameter.

    Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces.
    Also, it can contain '/' character and could break the use of os.path function.

    :param inputs_data: dict[string, dict[string, string]]
    """
    for key in inputs_data:
        inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"])


def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data):
    """
    Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
    and update the dictionary of datatype

    :param ExtensionClass:
    :param array_inputs:
    :param inputs_data:
    :type ExtensionClass: Datatype
    :type array_inputs: list[string]
    :type inputs_data: dict
    :rtype: dict
    """

    datatype_dictionary = {}

    # TODO: Optimize this double loop

            in STDOUT
        - Still access to full, brute and traceback for errors
            in STDERR
        - And further access to debug if needed
            in .log

    """

    if not log_stdout:
        raise Exception("No log_stdout given. Stopping the application")

    # stdout for INFO / WARN / ERROR / CRITICAL
    log_stdout.setLevel(logging.INFO)

    """
    Dev Logger is defined as following:
        - Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout
        - Still access to full, brute and traceback in stderr for errors
        - And further access to debug if needed

    """
    if not log_stdout:
        raise Exception("No log_stdout given. Stopping the application")
    log_format = '%(message)s'

    logging.getLogger().addHandler(log_stdout)

def configure_logger_stderr():
    """
    Configure what should be logged in stderr
    """
    log_error = logging.StreamHandler(sys.stderr)
    log_error.setLevel(logging.ERROR)
    log_error_format = '%(message)s'