logging

ensembl.utils.logging

Easy initialisation functionality to set an event logging system.

Examples:

>>> import logging, pathlib
>>> from ensembl.utils.logging import init_logging
>>> logfile = pathlib.Path("test.log")
>>> init_logging("INFO", logfile, "DEBUG")
>>> logging.info("This message is written in both stderr and the log file")
>>> logging.debug("This message is only written in the log file")

LogLevel = Union[int, str] module-attribute

init_logging(log_level='WARNING', log_file=None, log_file_level='DEBUG', msg_format='%(asctime)s\t%(levelname)s\t%(message)s', date_format='%Y-%m-%d_%H:%M:%S')

Initialises the logging system.

By default, all the log messages corresponding to log_level (and above) will be printed in the standard error. If log_file is provided, all messages of log_file_level level (and above) will be written into the provided file.

Parameters:

Name	Type	Description	Default
log_level	LogLevel	Minimum logging level for the standard error.	'WARNING'
log_file	Optional[StrPath]	Logging file where to write logging messages besides the standard error.	None
log_file_level	LogLevel	Minimum logging level for the logging file.	'DEBUG'
msg_format	str	A format string for the logged output as a whole. More information: https://docs.python.org/3/library/logging.html#logrecord-attributes	'%(asctime)s\t%(levelname)s\t%(message)s'
date_format	str	A format string for the date/time portion of the logged output. More information: https://docs.python.org/3/library/logging.html#logging.Formatter.formatTime	'%Y-%m-%d_%H:%M:%S'

Source code in src/ensembl/utils/logging.py

def init_logging(
    log_level: LogLevel = "WARNING",
    log_file: Optional[StrPath] = None,
    log_file_level: LogLevel = "DEBUG",
    msg_format: str = "%(asctime)s\t%(levelname)s\t%(message)s",
    date_format: str = r"%Y-%m-%d_%H:%M:%S",
) -> None:
    """Initialises the logging system.

    By default, all the log messages corresponding to `log_level` (and above) will be printed in the
    standard error. If `log_file` is provided, all messages of `log_file_level` level (and above) will
    be written into the provided file.

    Args:
        log_level: Minimum logging level for the standard error.
        log_file: Logging file where to write logging messages besides the standard error.
        log_file_level: Minimum logging level for the logging file.
        msg_format: A format string for the logged output as a whole. More information:
            https://docs.python.org/3/library/logging.html#logrecord-attributes
        date_format: A format string for the date/time portion of the logged output. More information:
            https://docs.python.org/3/library/logging.html#logging.Formatter.formatTime

    """
    # Configure the basic logging system, setting the root logger to the minimum log level available
    # to avoid filtering messages in any handler due to "parent delegation". Also close and remove any
    # existing handlers before setting this configuration.
    logging.basicConfig(format=msg_format, datefmt=date_format, level="DEBUG", force=True)
    # Set the correct log level of the new StreamHandler (by default it is set to NOTSET)
    logging.root.handlers[0].setLevel(log_level)
    if log_file:
        # Create the log file handler and add it to the root logger
        formatter = logging.Formatter(msg_format, datefmt=date_format)
        file_handler = logging.FileHandler(log_file)
        file_handler.setLevel(log_file_level)
        file_handler.setFormatter(formatter)
        logging.root.addHandler(file_handler)

init_logging_with_args(args)

Processes the Namespace object provided to call init_logging() with the correct arguments.

Parameters:

Name	Type	Description	Default
args	Namespace	Namespace populated by an argument parser.	required

Source code in src/ensembl/utils/logging.py

def init_logging_with_args(args: argparse.Namespace) -> None:
    """Processes the Namespace object provided to call `init_logging()` with the correct arguments.

    Args:
        args: Namespace populated by an argument parser.

    """
    args_dict = vars(args)
    log_args = {x: args_dict[x] for x in ["log_level", "log_file", "log_file_level"] if x in args_dict}
    init_logging(**log_args)