Source code for bioflow.utils.general_utils.high_level_os_io

Saner io and filesystem manipulation compared to python defaults
import os
from shutil import rmtree, copyfile
from bioflow.utils.log_behavior import get_logger

log = get_logger(__name__)

[docs]def mkdir_recursive(path): # pragma: no cover """ Recursively creates a directory that would contain a file given win-like filename ( or directory name :param path: :return: """ log.debug( 'trying to create recursively path containing: %s', path) path = os.path.abspath(path) directory_name = os.path.dirname(path) log.debug('subpath: %s', directory_name) if not os.path.exists(directory_name): mkdir_recursive(directory_name) if not os.path.exists(path): log.debug('path %s does not exist yet, looks like file: %s', path, '.' in path.split('/')[-1][-5:]) if '.' not in path.split('/')[-1][-5:]: # should be able to suppress specific file creation os.mkdir(path) log.debug('; created') else: log.debug('; creation skipped')
[docs]def wipe_dir(path): # pragma: no cover """ wipes the indicated directory :param path: :return: True on success """ path = os.path.abspath(path) log.debug('entered ') if not os.path.exists(path): log.debug('path does not exist') return True # Nothing to do: destruction already done if os.path.isdir(path): directory_name = path else: directory_name = os.path.dirname(path) log.debug('going to wipe %s for path %s', directory_name, path) if not os.path.isdir(directory_name): log.exception( 'failed to delete %s: for path %s, not a dir', directory_name, path) return False for sub_path in os.listdir(directory_name): if os.path.isdir(sub_path): log.exception( 'failed to delete %s: for path %s, anti rm -rf flag', directory_name, path) return False log.debug('performing a rmtree') rmtree(directory_name) return True
[docs]def copy_if_doesnt_exist(source, destination): # pragma: no cover """ Copies a file if it does not exist :param source: :param destination: :return: """ if not os.path.isfile(destination):'Did not detect file %s at the destination, copying from source %s' % (source, destination)) copyfile(source, destination)