biofx.utils package

Submodules

biofx.utils.LogUtils module

@cchng

Logging utilities that fulfill OMICS group requirements.

class biofx.utils.LogUtils.Masker(patterns)

Bases: logging.Filter

References

• http://stackoverflow.com/questions/879732/logging-with-filters
• https://www.relaxdiego.com/2014/07/logging-in-python.html

filter(record)

Filter and replaces record substring matching a pattern with asterisks.

Parameters:record – Returns:True Return type:bool

class biofx.utils.LogUtils.OMICSLogger

Bases: object

Logger based on OMICS code template.

exit_program()

Exit program.

static generate_status_file_names(outdir, program_name, prefix='', *status)

Generate status file names.

Parameters:

• outdir (string) – output directory path
• program_name (string) – program name
• prefix (string) – file prefix
• *status – status stamps as file extensions

Returns:

a tuple containing file names in the order of status provided

Return type:

tuple

get_current_time()

Get current time

init_logging(output_level=20, file_level=20, log_file_name=None, overwrite=False, logger_name='')

initialize the logging with default parameter. If use several time with same input file only the level of the logging will be change.

Parameters:

• output_level (int) – The logging level of output for the stdout. If set to None the stdout is not set or not changed. default: INFO.
• file_level (int) – The logging level of output for the log file. if set to None the logging in a file is not set or not changed. default: INFO.
• log_file_name (str) – The name of the file used for the logging. if set to None the logging in a file is not set or not changed. default: None.
• overwrite (bool) – if set to true an existing log file will overwritten, otherwise the next logg will be append. default: None.
• logger_name (string) – untested. DO NOT USE

Example

init_logging() –> set the stdout only to INFO init_logging(log_file_name=”any_file”) –> set the stdout and the log file to INFO init_logging(output_level=None, log_file_name=”any_file”) –> set the log file only to INFO don’t touch the stdout

log_end_time()

Log end time

log_run_info(program, version, dependencies, options=None)

Parameters:

• program (string) – name of program. usually file name
• version (string) – program version
• dependencies (dict) – a dictionary of dependency name as keys and dependency as values
• options (OptParser) – an instance of Optparser

static log_section(section, width=None, marker='=')

Formatted section string for logging. :param section: section name :type section: string :param width: screen width :type width: int :param marker: single character string to mark section :type marker: string

log_start_time()

Log start time

run_fail(failurefilename=None, exit_program=True, exit_status=1)

Fail analysis.

Parameters:

• failurefilename (string) – failure status file path
• exit_program (boolean) – exit program if True
• exit_status (int) – exit status. used if exit_program is True

run_incomplete(incompletefilename)

Incomplete analysis.

Parameters:incompletefilename (string) – incomplete status file path

run_success(successfilename, exit_program=True)

Successful analysis. Quits program with default status 0 when called.

Parameters:

• successfilename (string) – success status file path
• exit_program (bool) – True if exit program with 0 status.

biofx.utils.LogUtils.is_str(var)

Module contents