Source code for toil.lib.bioio

# Copyright (C) 2015-2021 Regents of the University of California
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import logging
import subprocess

from toil.statsAndLogging import logger, root_logger, set_logging_from_options
from toil.test import get_temp_file


# used by cactus
# TODO: only used in utilsTest.py; move this there once out of cactus
[docs] def system(command): """ A convenience wrapper around subprocess.check_call that logs the command before passing it on. The command can be either a string or a sequence of strings. If it is a string shell=True will be passed to subprocess.check_call. :type command: str | sequence[string] """ logger.warning('Deprecated toil method that will be moved/replaced in a future release."') logger.debug(f'Running: {command}') subprocess.check_call(command, shell=isinstance(command, str), bufsize=-1)
# Used by cactus; now a wrapper and not used in Toil. # TODO: Remove from cactus and then remove from Toil.
[docs] def getLogLevelString(logger=None): root_logger.warning('Deprecated toil method. Please call "logging.getLevelName" directly.') if logger is None: logger = root_logger return logging.getLevelName(logger.getEffectiveLevel())
# Used by cactus; now a wrapper and not used in Toil. # TODO: Remove from cactus and then remove from Toil.
[docs] def setLoggingFromOptions(options): logger.warning('Deprecated toil method. Please use "toil.statsAndLogging.set_logging_from_options()" instead."') set_logging_from_options(options)
# Used by cactus; now a wrapper and not used in Toil. # TODO: Remove from cactus and then remove from Toil.
[docs] def getTempFile(suffix="", rootDir=None): logger.warning('Deprecated toil method. Please use "toil.test.get_temp_file()" instead."') return get_temp_file(suffix, rootDir)