Log Messages

The ViennaRNA Package comes with a log message system that allows for filtering and (re-)routing of all messages issued by the library.

The default log message system prints messages that meet a certain log level to a file pointer that defaults to stderr. This file pointer, the log level threshold and the content of the messages can be adapted with the functions below.

In addition, the logging system allows for adding user-defined callbacks that can also retrieve the log messages for further processing. Along with that, the default logging mechanism can be turned off entirely such that only the callbacks process the log messages.

The example below demonstrates how log messages issued by RNAlib can be re-routed to the native Python logging module.

import RNA
import logging


# Set the default format and log-level for the Python `logging` module
logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.DEBUG)


def reroute_logs(e, data):
    """
    The wrapper callback function that receives RNAlib log messages
    and passes them through to the Python 'logging' module

    Parameters
    ----------

    e: dict
        A dictionary that contains the log message, the log level,
        as well as source code file and line number that issued the
        log message
    data: object
        A data object that is passed through to this callback
    """

    log_reroute = {
      RNA.LOG_LEVEL_ERROR: logging.error,
      RNA.LOG_LEVEL_WARNING: logging.warning,
      RNA.LOG_LEVEL_INFO: logging.info,
      RNA.LOG_LEVEL_DEBUG: logging.debug
    }

    # compose an example log message
    message = f"ViennaRNA: \"{e['message']}\" ({e['file_name']}:{e['line_number']})"

    # send log message to appropriate logging channel
    if e['level'] in log_reroute:
        log_reroute[e['level']](message)


# turn-off RNAlib self logging
RNA.log_level_set(RNA.LOG_LEVEL_SILENT)

# attach RNAlib logging to python logging and capture all
# logs with level at least DEBUG
RNA.log_cb_add(reroute_logs, level = RNA.LOG_LEVEL_DEBUG)


# compose an example call that might issue a few debug- or other
# log messages
md = RNA.md(circ=1, gquad=1)
s = RNA.random_string(10, "ACGU")

fc = RNA.fold_compound(s, md)

fc.mfe()