Source code for datalad.utils

# emacs: -*- mode: python; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-
# ex: set sts=4 ts=4 sw=4 noet:
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#   See COPYING file distributed along with the datalad package for the
#   copyright and license terms.
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import collections
import hashlib
import re
import six.moves.builtins as __builtin__
import time

import logging
import shutil
import os
import sys
import tempfile
import platform
import gc
import glob
import gzip
import string
import wrapt

from copy import copy as shallow_copy
from contextlib import contextmanager
from functools import wraps
from time import sleep
from inspect import getargspec
from itertools import tee

import os.path as op
from os.path import sep as dirsep
from os.path import commonprefix
from os.path import curdir, basename, exists, realpath, islink, join as opj
from os.path import isabs, normpath, expandvars, expanduser, abspath, sep
from os.path import isdir
from os.path import relpath
from os.path import stat
from os.path import dirname
from os.path import split as psplit
import posixpath

from six import PY2, text_type, binary_type, string_types

# from datalad.dochelpers import get_docstring_split
from datalad.consts import TIMESTAMP_FMT

if PY2:
    unicode_srctypes = string_types
    unicode_srctypes = string_types + (bytes,)

lgr = logging.getLogger("datalad.utils")

lgr.log(5, "Importing datalad.utils")
# Some useful variables
platform_system = platform.system().lower()
on_windows = platform_system == 'windows'
on_osx = platform_system == 'darwin'
on_linux = platform_system == 'linux'
on_msys_tainted_paths = on_windows \
                        and 'MSYS_NO_PATHCONV' not in os.environ \
                        and os.environ.get('MSYSTEM', '')[:4] in ('MSYS', 'MING')
    linux_distribution_name, linux_distribution_release \
        = platform.linux_distribution()[:2]
    on_debian_wheezy = on_linux \
                       and linux_distribution_name == 'debian' \
                       and linux_distribution_release.startswith('7.')
except:  # pragma: no cover
    # MIH: IndexError?
    on_debian_wheezy = False
    linux_distribution_name = linux_distribution_release = None

# Maximal length of cmdline string
# Query the system and use hardcoded "knowledge" if None
# probably   getconf ARG_MAX   might not be available
# The last one would be the most conservative/Windows
CMD_MAX_ARG_HARDCODED = 2097152 if on_linux else 262144 if on_osx else 32767
    CMD_MAX_ARG = os.sysconf('SC_ARG_MAX')
    assert CMD_MAX_ARG > 0
    if sys.version_info[:2] == (3, 4):
        # workaround for some kind of a bug which comes up with python 3.4
        # see
except Exception as exc:
    # ATM (20181005) SC_ARG_MAX available only on POSIX systems
    # so exception would be thrown e.g. on Windows, or
    # somehow during Debian build for nd14.04 it is coming up with -1:
        "Failed to query or got useless SC_ARG_MAX sysconf, "
        "will use hardcoded value: %s", exc)
# Even with all careful computations we do, due to necessity to account for
# environment and what not, we still could not figure out "exact" way to
# estimate it, but it was shown that 300k safety margin on linux was sufficient.
# 300k is ~15%, so to be safe, and for paranoid us we will just use up to 50%
# of the length for "safety margin".  We might probably still blow due to
# env vars, unicode, etc...  so any hard limit imho is not a proper solution
CMD_MAX_ARG = int(0.5 * CMD_MAX_ARG)
    "Maximal length of cmdline string (adjusted for safety margin): %d",

# Little helpers

[docs]def get_func_kwargs_doc(func): """ Provides args for a function Parameters ---------- func: str name of the function from which args are being requested Returns ------- list of the args that a function takes in """ return getargspec(func)[0]
# TODO: format error message with descriptions of args # return [repr(dict(get_docstring_split(func)[1]).get(x)) for x in getargspec(func)[0]]
[docs]def not_supported_on_windows(msg=None): """A little helper to be invoked to consistently fail whenever functionality is not supported (yet) on Windows """ if on_windows: raise NotImplementedError("This functionality is not yet implemented for Windows OS" + (": %s" % msg if msg else ""))
[docs]def shortened_repr(value, l=30): try: if hasattr(value, '__repr__') and (value.__repr__ is not object.__repr__): value_repr = repr(value) if not value_repr.startswith('<') and len(value_repr) > l: value_repr = "<<%s...>>" % (value_repr[:l - 8]) elif value_repr.startswith('<') and value_repr.endswith('>') and ' object at 0x': raise ValueError("I hate those useless long reprs") else: raise ValueError("gimme class") except Exception as e: value_repr = "<%s>" % value.__class__.__name__.split('.')[-1] return value_repr
def __auto_repr__(obj): attr_names = tuple() if hasattr(obj, '__dict__'): attr_names += tuple(obj.__dict__.keys()) if hasattr(obj, '__slots__'): attr_names += tuple(obj.__slots__) items = [] for attr in sorted(set(attr_names)): if attr.startswith('_'): continue value = getattr(obj, attr) # TODO: should we add this feature to minimize some talktative reprs # such as of URL? #if value is None: # continue items.append("%s=%s" % (attr, shortened_repr(value))) return "%s(%s)" % (obj.__class__.__name__, ', '.join(items))
[docs]def auto_repr(cls): """Decorator for a class to assign it an automagic quick and dirty __repr__ It uses public class attributes to prepare repr of a class Original idea: """ cls.__repr__ = __auto_repr__ return cls
def _is_stream_tty(stream): try: # TODO: check on windows if hasattr check would work correctly and # add value: return stream.isatty() except ValueError as exc: # Who knows why it is a ValueError, but let's try to be specific # If there is a problem with I/O - non-interactive, otherwise reraise if "I/O" in str(exc): return False raise
[docs]def is_interactive(): """Return True if all in/outs are open and tty. Note that in a somewhat abnormal case where e.g. stdin is explicitly closed, and any operation on it would raise a `ValueError("I/O operation on closed file")` exception, this function would just return False, since the session cannot be used interactively. """ return all(_is_stream_tty(s) for s in (sys.stdin, sys.stdout, sys.stderr))
[docs]def get_ipython_shell(): """Detect if running within IPython and returns its `ip` (shell) object Returns None if not under ipython (no `get_ipython` function) """ try: return get_ipython() except NameError: return None
[docs]def md5sum(filename): """Compute an MD5 sum for the given file """ from import Digester return Digester(digests=['md5'])(filename)['md5']
[docs]def sorted_files(dout): """Return a (sorted) list of files under dout """ return sorted(sum([[opj(r, f)[len(dout) + 1:] for f in files] for r, d, files in os.walk(dout) if not '.git' in r], []))
_VCS_REGEX = r'%s\.(?:git|gitattributes|svn|bzr|hg)(?:%s|$)' % (dirsep, dirsep) _DATALAD_REGEX = r'%s\.(?:datalad)(?:%s|$)' % (dirsep, dirsep)
[docs]def find_files(regex, topdir=curdir, exclude=None, exclude_vcs=True, exclude_datalad=False, dirs=False): """Generator to find files matching regex Parameters ---------- regex: basestring exclude: basestring, optional Matches to exclude exclude_vcs: If True, excludes commonly known VCS subdirectories. If string, used as regex to exclude those files (regex: `%r`) exclude_datalad: If True, excludes files known to be datalad meta-data files (e.g. under .datalad/ subdirectory) (regex: `%r`) topdir: basestring, optional Directory where to search dirs: bool, optional Whether to match directories as well as files """ for dirpath, dirnames, filenames in os.walk(topdir): names = (dirnames + filenames) if dirs else filenames # TODO: might want to uniformize on windows to use '/' paths = (opj(dirpath, name) for name in names) for path in filter(re.compile(regex).search, paths): path = path.rstrip(dirsep) if exclude and, path): continue if exclude_vcs and, path): continue if exclude_datalad and, path): continue yield path
find_files.__doc__ %= (_VCS_REGEX, _DATALAD_REGEX)
[docs]def expandpath(path, force_absolute=True): """Expand all variables and user handles in a path. By default return an absolute path """ path = expandvars(expanduser(path)) if force_absolute: path = abspath(path) return path
[docs]def posix_relpath(path, start=None): """Behave like os.path.relpath, but always return POSIX paths... on any platform.""" # join POSIX style return posixpath.join( # split and relpath native style # python2.7 ntpath implementation of relpath cannot handle start=None *psplit( relpath(path, start=start if start is not None else '')))
[docs]def is_explicit_path(path): """Return whether a path explicitly points to a location Any absolute path, or relative path starting with either '../' or './' is assumed to indicate a location on the filesystem. Any other path format is not considered explicit.""" path = expandpath(path, force_absolute=False) return isabs(path) \ or path.startswith(os.curdir + os.sep) \ or path.startswith(os.pardir + os.sep)
# handle this dance once, and import pathlib from here # in all other places if PY2: from pathlib2 import ( Path, PurePath, PurePosixPath, ) def _unicode_path(pathobj): return assure_unicode(str(pathobj)) PurePath.__unicode__ = _unicode_path else: from pathlib import ( Path, PurePath, PurePosixPath, )
[docs]def rotree(path, ro=True, chmod_files=True): """To make tree read-only or writable Parameters ---------- path : string Path to the tree/directory to chmod ro : bool, optional Whether to make it R/O (default) or RW chmod_files : bool, optional Whether to operate also on files (not just directories) """ if ro: chmod = lambda f: os.chmod(f, os.stat(f).st_mode & ~stat.S_IWRITE) else: chmod = lambda f: os.chmod(f, os.stat(f).st_mode | stat.S_IWRITE | stat.S_IREAD) for root, dirs, files in os.walk(path, followlinks=False): if chmod_files: for f in files: fullf = opj(root, f) # might be the "broken" symlink which would fail to stat etc if exists(fullf): chmod(fullf) chmod(root)
[docs]def rmtree(path, chmod_files='auto', children_only=False, *args, **kwargs): """To remove git-annex .git it is needed to make all files and directories writable again first Parameters ---------- chmod_files : string or bool, optional Whether to make files writable also before removal. Usually it is just a matter of directories to have write permissions. If 'auto' it would chmod files on windows by default children_only : bool, optional If set, all files and subdirectories would be removed while the path itself (must be a directory) would be preserved `*args` : `**kwargs` : Passed into shutil.rmtree call """ # Give W permissions back only to directories, no need to bother with files if chmod_files == 'auto': chmod_files = on_windows # TODO: yoh thinks that if we could quickly check our Flyweight for # repos if any of them is under the path, and could call .precommit # on those to possibly stop batched processes etc, we did not have # to do it on case by case # Check for open files assert_no_open_files(path) if children_only: if not os.path.isdir(path): raise ValueError("Can remove children only of directories") for p in os.listdir(path): rmtree(op.join(path, p)) return if not (os.path.islink(path) or not os.path.isdir(path)): rotree(path, ro=False, chmod_files=chmod_files) _rmtree(path, *args, **kwargs) else: # just remove the symlink unlink(path)
[docs]def rmdir(path, *args, **kwargs): """os.rmdir with our optional checking for open files""" assert_no_open_files(path) os.rmdir(path)
[docs]def get_open_files(path, log_open=False): """Get open files under a path Parameters ---------- path : str File or directory to check for open files under log_open : bool or int If set - logger level to use Returns ------- dict path : pid """ # Original idea: import psutil files = {} # since the ones returned by psutil would not be aware of symlinks in the # path we should also get realpath for path path = realpath(path) for proc in psutil.process_iter(): try: open_paths = [p.path for p in proc.open_files()] + [proc.cwd()] for p in open_paths: # note: could be done more efficiently so we do not # renormalize path over and over again etc if path_startswith(p, path): files[p] = proc # Catch a race condition where a process ends # before we can examine its files except psutil.NoSuchProcess: pass except psutil.AccessDenied: pass if files and log_open: lgr.log(log_open, "Open files under %s: %s", path, files) return files
_assert_no_open_files_cfg = os.environ.get('DATALAD_ASSERT_NO_OPEN_FILES') if _assert_no_open_files_cfg: def assert_no_open_files(path): files = get_open_files(path, log_open=40) if _assert_no_open_files_cfg == 'assert': assert not files elif files: if _assert_no_open_files_cfg == 'pdb': import pdb pdb.set_trace() elif _assert_no_open_files_cfg == 'epdb': import epdb epdb.serve() pass # otherwise we would just issue that error message in the log else:
[docs] def assert_no_open_files(*args, **kwargs): pass
[docs]def rmtemp(f, *args, **kwargs): """Wrapper to centralize removing of temp files so we could keep them around It will not remove the temporary file/directory if DATALAD_TESTS_TEMP_KEEP environment variable is defined """ if not os.environ.get('DATALAD_TESTS_TEMP_KEEP'): if not os.path.lexists(f): lgr.debug("Path %s does not exist, so can't be removed" % f) return lgr.log(5, "Removing temp file: %s" % f) # Can also be a directory if os.path.isdir(f): rmtree(f, *args, **kwargs) else: unlink(f) else:"Keeping temp file: %s" % f)
[docs]def file_basename(name, return_ext=False): """ Strips up to 2 extensions of length up to 4 characters and starting with alpha not a digit, so we could get rid of .tar.gz etc """ bname = basename(name) fbname = re.sub(r'(\.[a-zA-Z_]\S{1,4}){0,2}$', '', bname) if return_ext: return fbname, bname[len(fbname) + 1:] else: return fbname
[docs]def escape_filename(filename): """Surround filename in "" and escape " in the filename """ filename = filename.replace('"', r'\"').replace('`', r'\`') filename = '"%s"' % filename return filename
[docs]def encode_filename(filename): """Encode unicode filename """ if isinstance(filename, text_type): return filename.encode(sys.getfilesystemencoding()) else: return filename
[docs]def decode_input(s): """Given input string/bytes, decode according to stdin codepage (or UTF-8) if not defined If fails -- issue warning and decode allowing for errors being replaced """ if isinstance(s, text_type): return s else: encoding = sys.stdin.encoding or 'UTF-8' try: return s.decode(encoding) except UnicodeDecodeError as exc: lgr.warning( "Failed to decode input string using %s encoding. " "Decoding allowing for errors", encoding) return s.decode(encoding, errors='replace')
if on_windows: def lmtime(filepath, mtime): """Set mtime for files. On Windows a merely adapter to os.utime """ os.utime(filepath, (time.time(), mtime)) else:
[docs] def lmtime(filepath, mtime): """Set mtime for files, while not de-referencing symlinks. To overcome absence of os.lutime Works only on linux and OSX ATM """ from .cmd import Runner # convert mtime to format touch understands [[CC]YY]MMDDhhmm[.SS] smtime = time.strftime("%Y%m%d%H%M.%S", time.localtime(mtime)) lgr.log(3, "Setting mtime for %s to %s == %s", filepath, mtime, smtime) Runner().run(['touch', '-h', '-t', '%s' % smtime, filepath]) rfilepath = realpath(filepath) if islink(filepath) and exists(rfilepath): # trust noone - adjust also of the target file # since it seemed like downloading under OSX (was it using curl?) # didn't bother with timestamps lgr.log(3, "File is a symlink to %s Setting mtime for it to %s", rfilepath, mtime) os.utime(rfilepath, (time.time(), mtime))
# doesn't work on OSX # Runner().run(['touch', '-h', '-d', '@%s' % mtime, filepath])
[docs]def assure_tuple_or_list(obj): """Given an object, wrap into a tuple if not list or tuple """ if isinstance(obj, (list, tuple)): return obj return (obj,)
[docs]def assure_iter(s, cls, copy=False, iterate=True): """Given not a list, would place it into a list. If None - empty list is returned Parameters ---------- s: list or anything cls: class Which iterable class to assure copy: bool, optional If correct iterable is passed, it would generate its shallow copy iterate: bool, optional If it is not a list, but something iterable (but not a text_type) iterate over it. """ if isinstance(s, cls): return s if not copy else shallow_copy(s) elif isinstance(s, text_type): return cls((s,)) elif iterate and hasattr(s, '__iter__'): return cls(s) elif s is None: return cls() else: return cls((s,))
[docs]def assure_list(s, copy=False, iterate=True): """Given not a list, would place it into a list. If None - empty list is returned Parameters ---------- s: list or anything copy: bool, optional If list is passed, it would generate a shallow copy of the list iterate: bool, optional If it is not a list, but something iterable (but not a text_type) iterate over it. """ return assure_iter(s, list, copy=copy, iterate=iterate)
[docs]def assure_list_from_str(s, sep='\n'): """Given a multiline string convert it to a list of return None if empty Parameters ---------- s: str or list """ if not s: return None if isinstance(s, list): return s return s.split(sep)
[docs]def assure_dict_from_str(s, **kwargs): """Given a multiline string with key=value items convert it to a dictionary Parameters ---------- s: str or dict Returns None if input s is empty """ if not s: return None if isinstance(s, dict): return s out = {} for value_str in assure_list_from_str(s, **kwargs): if '=' not in value_str: raise ValueError("{} is not in key=value format".format(repr(value_str))) k, v = value_str.split('=', 1) if k in out: err = "key {} was already defined in {}, but new value {} was provided".format(k, out, v) raise ValueError(err) out[k] = v return out
[docs]def assure_bytes(s, encoding='utf-8'): """Convert/encode unicode to str (PY2) or bytes (PY3) if of 'text_type' Parameters ---------- encoding: str, optional Encoding to use. "utf-8" is the default """ if not isinstance(s, text_type): return s return s.encode(encoding)
[docs]def assure_unicode(s, encoding=None, confidence=None): """Convert/decode to unicode (PY2) or str (PY3) if of 'binary_type' Parameters ---------- encoding: str, optional Encoding to use. If None, "utf-8" is tried, and then if not a valid UTF-8, encoding will be guessed confidence: float, optional A value between 0 and 1, so if guessing of encoding is of lower than specified confidence, ValueError is raised """ if not isinstance(s, binary_type): return s if encoding is None: # Figure out encoding, defaulting to 'utf-8' which is our common # target in contemporary digital society try: return s.decode('utf-8') except UnicodeDecodeError as exc: from .dochelpers import exc_str lgr.debug("Failed to decode a string as utf-8: %s", exc_str(exc)) # And now we could try to guess from chardet import detect enc = detect(s) denc = enc.get('encoding', None) if denc: denc_confidence = enc.get('confidence', 0) if confidence is not None and denc_confidence < confidence: raise ValueError( "Failed to auto-detect encoding with high enough " "confidence. Highest confidence was %s for %s" % (denc_confidence, denc) ) return s.decode(denc) else: raise ValueError( "Could not decode value as utf-8, or to guess its encoding: %s" % repr(s) ) else: return s.decode(encoding)
[docs]def assure_bool(s): """Convert value into boolean following convention for strings to recognize on,True,yes as True, off,False,no as False """ if isinstance(s, string_types): if s.isdigit(): return bool(int(s)) sl = s.lower() if sl in {'y', 'yes', 'true', 'on'}: return True elif sl in {'n', 'no', 'false', 'off'}: return False else: raise ValueError("Do not know how to treat %r as a boolean" % s) return bool(s)
[docs]def as_unicode(val, cast_types=object): """Given an arbitrary value, would try to obtain unicode value of it For unicode it would return original value, for python2 str or python3 bytes it would use assure_unicode, for None - an empty (unicode) string, and for any other type (see `cast_types`) - would apply the unicode constructor. If value is not an instance of `cast_types`, TypeError is thrown Parameters ---------- cast_types: type Which types to cast to unicode by providing to constructor """ if val is None: return u'' elif isinstance(val, text_type): return val elif isinstance(val, unicode_srctypes): return assure_unicode(val) elif isinstance(val, cast_types): return text_type(val) else: raise TypeError( "Value %r is not of any of known or provided %s types" % (val, cast_types))
[docs]def unique(seq, key=None, reverse=False): """Given a sequence return a list only with unique elements while maintaining order This is the fastest solution. See and for more information. Enhancement -- added ability to compare for uniqueness using a key function Parameters ---------- seq: Sequence to analyze key: callable, optional Function to call on each element so we could decide not on a full element, but on its member etc reverse: bool, optional If True, uniqueness checked in the reverse order, so that the later ones will take the order """ seen = set() seen_add = seen.add trans = reversed if reverse else lambda x: x if not key: out = [x for x in trans(seq) if not (x in seen or seen_add(x))] else: # OPT: could be optimized, since key is called twice, but for our cases # should be just as fine out = [x for x in trans(seq) if not (key(x) in seen or seen_add(key(x)))] return out[::-1] if reverse else out
[docs]def all_same(items): """Quick check if all items are the same. Identical to a check like len(set(items)) == 1 but should be more efficient while working on generators, since would return False as soon as any difference detected thus possibly avoiding unnecessary evaluations """ first = True first_item = None for item in items: if first: first = False first_item = item else: if item != first_item: return False # So we return False if was empty return not first
[docs]def map_items(func, v): """A helper to apply `func` to all elements (keys and values) within dict No type checking of values passed to func is done, so `func` should be resilient to values which it should not handle Initial usecase - apply_recursive(url_fragment, assure_unicode) """ # map all elements within item return v.__class__( item.__class__(map(func, item)) for item in v.items() )
[docs]def partition(items, predicate=bool): """Partition `items` by `predicate`. Parameters ---------- items : iterable predicate : callable A function that will be mapped over each element in `items`. The elements will partitioned based on whether the return value is false or true. Returns ------- A tuple with two generators, the first for 'false' items and the second for 'true' ones. Notes ----- Taken from Peter Otten's snippet posted at """ a, b = tee((predicate(item), item) for item in items) return ((item for pred, item in a if not pred), (item for pred, item in b if pred))
[docs]def generate_chunks(container, size): """Given a container, generate chunks from it with size up to `size` """ # There could be a "smarter" solution but I think this would suffice assert size > 0, "Size should be non-0 positive" while container: yield container[:size] container = container[size:]
[docs]def generate_file_chunks(files, cmd=None): """Given a list of files, generate chunks of them to avoid exceding cmdline length Parameters ---------- files: list of str cmd: str or list of str, optional Command to account for as well """ files = assure_list(files) cmd = assure_list(cmd) maxl = max(map(len, files)) if files else 0 chunk_size = max( 1, # should at least be 1. If blows then - not our fault (CMD_MAX_ARG - sum((len(x) + 3) for x in cmd) - 4 # for '--' below ) // (maxl + 3) # +3 for possible quotes and a space ) # TODO: additional treatment for "too many arguments"? although # as # -436272758 # shows there seems to be no hardcoded limit on # of arguments, # but may be we decide to go for smth like follow to be on safe side # chunk_size = min(10240 - len(cmd), chunk_size) file_chunks = generate_chunks(files, chunk_size) return file_chunks
# # Generators helpers #
[docs]def saved_generator(gen): """Given a generator returns two generators, where 2nd one just replays So the first one would be going through the generated items and 2nd one would be yielding saved items """ saved = [] def gen1(): for x in gen: # iterating over original generator saved.append(x) yield x def gen2(): for x in saved: # yielding saved entries yield x return gen1(), gen2()
# # Decorators #
[docs]def better_wraps(to_be_wrapped): """Decorator to replace `functools.wraps` This is based on `wrapt` instead of `functools` and in opposition to `wraps` preserves the correct signature of the decorated function. It is written with the intention to replace the use of `wraps` without any need to rewrite the actual decorators. """ @wrapt.decorator(adapter=to_be_wrapped) def intermediator(to_be_wrapper, instance, args, kwargs): return to_be_wrapper(*args, **kwargs) return intermediator
# Borrowed from pandas # Copyright: 2011-2014, Lambda Foundry, Inc. and PyData Development Team # License: BSD-3
[docs]def optional_args(decorator): """allows a decorator to take optional positional and keyword arguments. Assumes that taking a single, callable, positional argument means that it is decorating a function, i.e. something like this:: @my_decorator def function(): pass Calls decorator with decorator(f, `*args`, `**kwargs`)""" @better_wraps(decorator) def wrapper(*args, **kwargs): def dec(f): return decorator(f, *args, **kwargs) is_decorating = not kwargs and len(args) == 1 and isinstance(args[0], collections.Callable) if is_decorating: f = args[0] args = [] return dec(f) else: return dec return wrapper
# TODO: just provide decorators for* functions. This is ugly!
[docs]def get_tempfile_kwargs(tkwargs=None, prefix="", wrapped=None): """Updates kwargs to be passed to tempfile. calls depending on env vars """ if tkwargs is None: tkwargs_ = {} else: # operate on a copy of tkwargs to avoid any side-effects tkwargs_ = tkwargs.copy() # TODO: don't remember why I had this one originally # if len(targs)<2 and \ if 'prefix' not in tkwargs_: tkwargs_['prefix'] = '_'.join( ['datalad_temp'] + ([prefix] if prefix else []) + ([''] if (on_windows or not wrapped) else [wrapped.__name__])) directory = os.environ.get('DATALAD_TESTS_TEMP_DIR') if directory and 'dir' not in tkwargs_: tkwargs_['dir'] = directory return tkwargs_
[docs]@optional_args def line_profile(func): """Q&D helper to line profile the function and spit out stats """ import line_profiler prof = line_profiler.LineProfiler() @wraps(func) def newfunc(*args, **kwargs): try: pfunc = prof(func) return pfunc(*args, **kwargs) finally: prof.print_stats() return newfunc
# Borrowed from duecredit to wrap duecredit-handling to guarantee failsafe
[docs]def never_fail(f): """Assure that function never fails -- all exceptions are caught Returns `None` if function fails internally. """ @wraps(f) def wrapped_func(*args, **kwargs): try: return f(*args, **kwargs) except Exception as e: lgr.warning( "DataLad internal failure while running %s: %r. " "Please report at" % (f, e) ) if os.environ.get('DATALAD_ALLOW_FAIL', False): return f else: return wrapped_func
# # Context Managers #
[docs]@contextmanager def nothing_cm(): """Just a dummy cm to programmically switch context managers""" yield
[docs]@contextmanager def swallow_outputs(): """Context manager to help consuming both stdout and stderr, and print() stdout is available as cm.out and stderr as cm.err whenever cm is the yielded context manager. Internally uses temporary files to guarantee absent side-effects of swallowing into StringIO which lacks .fileno. print mocking is necessary for some uses where sys.stdout was already bound to original sys.stdout, thus mocking it later had no effect. Overriding print function had desired effect """ class StringIOAdapter(object): """Little adapter to help getting out/err values """ def __init__(self): kw = get_tempfile_kwargs({}, prefix="outputs") self._out = open(tempfile.mktemp(**kw), 'w') self._err = open(tempfile.mktemp(**kw), 'w') def _read(self, h): with open( as f: return @property def out(self): if not self._out.closed: self._out.flush() return self._read(self._out) @property def err(self): if not self._err.closed: self._err.flush() return self._read(self._err) @property def handles(self): return self._out, self._err def cleanup(self): self._out.close() self._err.close() out_name = err_name = del self._out del self._err gc.collect() rmtemp(out_name) rmtemp(err_name) def fake_print(*args, **kwargs): sep = kwargs.pop('sep', ' ') end = kwargs.pop('end', '\n') file = kwargs.pop('file', sys.stdout) if file in (oldout, olderr, sys.stdout, sys.stderr): # we mock try: sys.stdout.write(sep.join(args) + end) except UnicodeEncodeError as exc: lgr.error( "Failed to write to mocked stdout, got %s, continue as it " "didn't happen", exc) else: # must be some other file one -- leave it alone oldprint(*args, sep=sep, end=end, file=file) from .ui import ui # preserve -- they could have been mocked already oldprint = getattr(__builtin__, 'print') oldout, olderr = sys.stdout, sys.stderr olduiout = ui.out adapter = StringIOAdapter() try: sys.stdout, sys.stderr = adapter.handles ui.out = adapter.handles[0] setattr(__builtin__, 'print', fake_print) yield adapter finally: sys.stdout, sys.stderr, ui.out = oldout, olderr, olduiout setattr(__builtin__, 'print', oldprint) adapter.cleanup()
[docs]@contextmanager def swallow_logs(new_level=None, file_=None, name='datalad'): """Context manager to consume all logs. """ lgr = logging.getLogger(name) # Keep old settings old_level = lgr.level old_handlers = lgr.handlers # Let's log everything into a string # TODO: generalize with the one for swallow_outputs class StringIOAdapter(object): """Little adapter to help getting out values And to stay consistent with how swallow_outputs behaves """ def __init__(self): if file_ is None: kw = get_tempfile_kwargs({}, prefix="logs") out_file = tempfile.mktemp(**kw) else: out_file = file_ # PY3 requires clearly one or another. race condition possible self._out = open(out_file, 'a') self._final_out = None def _read(self, h): with open( as f: return @property def out(self): if self._final_out is not None: # we closed and cleaned up already return self._final_out else: self._out.flush() return self._read(self._out) @property def lines(self): return self.out.split('\n') @property def handle(self): return self._out def cleanup(self): # store for access while object exists self._final_out = self.out self._out.close() out_name = del self._out gc.collect() if not file_: rmtemp(out_name) def assert_logged(self, msg=None, level=None, regex=True, **kwargs): """Provide assertion on whether a msg was logged at a given level If neither `msg` nor `level` provided, checks if anything was logged at all. Parameters ---------- msg: str, optional Message (as a regular expression, if `regex`) to be searched. If no msg provided, checks if anything was logged at a given level. level: str, optional String representing the level to be logged regex: bool, optional If False, regular `assert_in` is used **kwargs: str, optional Passed to `assert_re_in` or `assert_in` """ from datalad.tests.utils import assert_re_in from datalad.tests.utils import assert_in if regex: match = r'\[%s\] ' % level if level else r"\[\S+\] " else: match = '[%s] ' % level if level else '' if msg: match += msg if match: (assert_re_in if regex else assert_in)(match, self.out, **kwargs) else: assert not kwargs, "no kwargs to be passed anywhere" assert self.out, "Nothing was logged!?" adapter = StringIOAdapter() # TODO: it does store messages but without any formatting, i.e. even without # date/time prefix etc. IMHO it should preserve formatting in case if file_ is # set swallow_handler = logging.StreamHandler(adapter.handle) # we want to log levelname so we could test against it swallow_handler.setFormatter( logging.Formatter('[%(levelname)s] %(message)s')) # Inherit filters from datalad.log import ProgressHandler swallow_handler.filters = sum([h.filters for h in old_handlers if not isinstance(h, ProgressHandler)], []) lgr.handlers = [swallow_handler] if old_level < logging.DEBUG: # so if HEAVYDEBUG etc -- show them! lgr.handlers += old_handlers if isinstance(new_level, str): new_level = getattr(logging, new_level) if new_level is not None: lgr.setLevel(new_level) try: yield adapter # TODO: if file_ and there was an exception -- most probably worth logging it? # although ideally it should be the next log outside added to that file_ ... oh well finally: lgr.handlers, lgr.level = old_handlers, old_level adapter.cleanup()
# TODO: May be melt in with swallow_logs at some point:
[docs]@contextmanager def disable_logger(logger=None): """context manager to temporarily disable logging This is to provide one of swallow_logs' purposes without unnecessarily creating temp files (see gh-1865) Parameters ---------- logger: Logger Logger whose handlers will be ordered to not log anything. Default: datalad's topmost Logger ('datalad') """ class NullFilter(logging.Filter): """Filter class to reject all records """ def filter(self, record): return 0 if logger is None: # default: all of datalad's logging: logger = logging.getLogger('datalad') filter_ = NullFilter( [h.addFilter(filter_) for h in logger.handlers] try: yield logger finally: [h.removeFilter(filter_) for h in logger.handlers]
# # Additional handlers # _sys_excepthook = sys.excepthook # Just in case we ever need original one
[docs]def setup_exceptionhook(ipython=False): """Overloads default sys.excepthook with our exceptionhook handler. If interactive, our exceptionhook handler will invoke pdb.post_mortem; if not interactive, then invokes default handler. """ def _datalad_pdb_excepthook(type, value, tb): import traceback traceback.print_exception(type, value, tb) print() if is_interactive(): import pdb pdb.post_mortem(tb) if ipython: from IPython.core import ultratb sys.excepthook = ultratb.FormattedTB(mode='Verbose', # color_scheme='Linux', call_pdb=is_interactive()) else: sys.excepthook = _datalad_pdb_excepthook
[docs]def assure_dir(*args): """Make sure directory exists. Joins the list of arguments to an os-specific path to the desired directory and creates it, if it not exists yet. """ dirname = opj(*args) if not exists(dirname): os.makedirs(dirname) return dirname
[docs]def updated(d, update): """Return a copy of the input with the 'update' Primarily for updating dictionaries """ d = d.copy() d.update(update) return d
_pwd_mode = None def _switch_to_getcwd(msg, *args): global _pwd_mode _pwd_mode = 'cwd' lgr.warning( msg + ". From now on will be returning os.getcwd(). Directory" " symlinks in the paths will be resolved", *args ) # TODO: we might want to mitigate by going through all flywheighted # repos and tuning up their .paths to be resolved?
[docs]def getpwd(): """Try to return a CWD without dereferencing possible symlinks This function will try to use PWD environment variable to provide a current working directory, possibly with some directories along the path being symlinks to other directories. Unfortunately, PWD is used/set only by the shell and such functions as `os.chdir` and `os.getcwd` nohow use or modify it, thus `os.getcwd()` returns path with links dereferenced. While returning current working directory based on PWD env variable we verify that the directory is the same as `os.getcwd()` after resolving all symlinks. If that verification fails, we fall back to always use `os.getcwd()`. Initial decision to either use PWD env variable or os.getcwd() is done upon the first call of this function. """ global _pwd_mode if _pwd_mode is None: # we need to decide! try: pwd = os.environ['PWD'] if on_windows and pwd and pwd.startswith('/'): # It should be a path from MSYS. # - it might start with a drive letter or not # - it seems to be "illegal" to have a single letter directories # under / path, i.e. if created - they aren't found # - 'ln -s' does not fail to create a "symlink" but it just # copies! # so we are not likely to need original PWD purpose on # those systems # Verdict: _pwd_mode = 'cwd' else: _pwd_mode = 'PWD' except KeyError: _pwd_mode = 'cwd' if _pwd_mode == 'cwd': return os.getcwd() elif _pwd_mode == 'PWD': try: cwd = os.getcwd() except OSError as exc: if "o such file" in str(exc): # directory was removed but we promised to be robust and # still report the path we might know since we are still in PWD # mode cwd = None else: raise try: pwd = os.environ['PWD'] pwd_real = op.realpath(pwd) # This logic would fail to catch the case where chdir did happen # to the directory where current PWD is pointing to, e.g. # $> ls -ld $PWD # lrwxrwxrwx 1 yoh yoh 5 Oct 11 13:27 /home/yoh/.tmp/tmp -> /tmp// # hopa:~/.tmp/tmp # $> python -c 'import os; os.chdir("/tmp"); from datalad.utils import getpwd; print(getpwd(), os.getcwd())' # ('/home/yoh/.tmp/tmp', '/tmp') # but I guess that should not be too harmful if cwd is not None and pwd_real != cwd: _switch_to_getcwd( "realpath of PWD=%s is %s whenever os.getcwd()=%s", pwd, pwd_real, cwd ) return cwd return pwd except KeyError: _switch_to_getcwd("PWD env variable is no longer available") return cwd # Must not happen, but may be someone # evil purges PWD from environ? else: raise RuntimeError( "Must have not got here. " "pwd_mode must be either cwd or PWD. And it is now %r" % (_pwd_mode,) )
[docs]class chpwd(object): """Wrapper around os.chdir which also adjusts environ['PWD'] The reason is that otherwise PWD is simply inherited from the shell and we have no ability to assess directory path without dereferencing symlinks. If used as a context manager it allows to temporarily change directory to the given path """ def __init__(self, path, mkdir=False, logsuffix=''): if path: pwd = getpwd() self._prev_pwd = pwd else: self._prev_pwd = None return if not isabs(path): path = normpath(opj(pwd, path)) if not os.path.exists(path) and mkdir: self._mkdir = True os.mkdir(path) else: self._mkdir = False lgr.debug("chdir %r -> %r %s", self._prev_pwd, path, logsuffix) os.chdir(path) # for grep people -- ok, to chdir here! os.environ['PWD'] = assure_bytes(path) if PY2 else path def __enter__(self): # nothing more to do really, chdir was in the constructor pass def __exit__(self, exc_type, exc_val, exc_tb): if self._prev_pwd: # Need to use self.__class__ so this instance, if the entire # thing mocked during the test, still would use correct chpwd self.__class__(self._prev_pwd, logsuffix="(coming back)")
[docs]def dlabspath(path, norm=False): """Symlinks-in-the-cwd aware abspath os.path.abspath relies on os.getcwd() which would not know about symlinks in the path TODO: we might want to norm=True by default to match behavior of os .path.abspath? """ if not isabs(path): # if not absolute -- relative to pwd path = opj(getpwd(), path) return normpath(path) if norm else path
[docs]def with_pathsep(path): """Little helper to guarantee that path ends with /""" return path + sep if not path.endswith(sep) else path
[docs]def get_path_prefix(path, pwd=None): """Get path prefix (for current directory) Returns relative path to the topdir, if we are under topdir, and if not absolute path to topdir. If `pwd` is not specified - current directory assumed """ pwd = pwd or getpwd() path = dlabspath(path) path_ = with_pathsep(path) pwd_ = with_pathsep(pwd) common = commonprefix((path_, pwd_)) if common.endswith(sep) and common in {path_, pwd_}: # we are in subdir or above the path = use relative path location_prefix = relpath(path, pwd) # if benign "here" - cut off if location_prefix in (curdir, curdir + sep): location_prefix = '' return location_prefix else: # just return absolute path return path
def _get_normalized_paths(path, prefix): if isabs(path) != isabs(prefix): raise ValueError("Both paths must either be absolute or relative. " "Got %r and %r" % (path, prefix)) path = with_pathsep(path) prefix = with_pathsep(prefix) return path, prefix
[docs]def path_startswith(path, prefix): """Return True if path starts with prefix path Parameters ---------- path: str prefix: str """ path, prefix = _get_normalized_paths(path, prefix) return path.startswith(prefix)
[docs]def path_is_subpath(path, prefix): """Return True if path is a subpath of prefix It will return False if path == prefix. Parameters ---------- path: str prefix: str """ path, prefix = _get_normalized_paths(path, prefix) return (len(prefix) < len(path)) and path.startswith(prefix)
[docs]def knows_annex(path): """Returns whether at a given path there is information about an annex It is just a thin wrapper around GitRepo.is_with_annex() classmethod which also checks for `path` to exist first. This includes actually present annexes, but also uninitialized ones, or even the presence of a remote annex branch. """ from os.path import exists if not exists(path): lgr.debug("No annex: test path {0} doesn't exist".format(path)) return False from import GitRepo return GitRepo(path, init=False, create=False).is_with_annex()
[docs]@contextmanager def make_tempfile(content=None, wrapped=None, **tkwargs): """Helper class to provide a temporary file name and remove it at the end (context manager) Parameters ---------- mkdir : bool, optional (default: False) If True, temporary directory created using tempfile.mkdtemp() content : str or bytes, optional Content to be stored in the file created wrapped : function, optional If set, function name used to prefix temporary file name `**tkwargs`: All other arguments are passed into the call to{,d}temp(), and resultant temporary filename is passed as the first argument into the function t. If no 'prefix' argument is provided, it will be constructed using module and function names ('.' replaced with '_'). To change the used directory without providing keyword argument 'dir' set DATALAD_TESTS_TEMP_DIR. Examples -------- >>> from os.path import exists >>> from datalad.utils import make_tempfile >>> with make_tempfile() as fname: ... k = open(fname, 'w').write('silly test') >>> assert not exists(fname) # was removed >>> with make_tempfile(content="blah") as fname: ... assert open(fname).read() == "blah" """ if tkwargs.get('mkdir', None) and content is not None: raise ValueError("mkdir=True while providing content makes no sense") tkwargs_ = get_tempfile_kwargs(tkwargs, wrapped=wrapped) # if DATALAD_TESTS_TEMP_DIR is set, use that as directory, # let mktemp handle it otherwise. However, an explicitly provided # dir=... will override this. mkdir = tkwargs_.pop('mkdir', False) filename = {False: tempfile.mktemp, True: tempfile.mkdtemp}[mkdir](**tkwargs_) filename = realpath(filename) if content: with open(filename, 'w' + ('b' if isinstance(content, binary_type) else '')) as f: f.write(content) if __debug__: # TODO mkdir lgr.debug('Created temporary thing named %s"' % filename) try: yield filename finally: # glob here for all files with the same name (-suffix) # would be useful whenever we requested .img filename, # and function creates .hdr as well lsuffix = len(tkwargs_.get('suffix', '')) filename_ = lsuffix and filename[:-lsuffix] or filename filenames = glob.glob(filename_ + '*') if len(filename_) < 3 or len(filenames) > 5: # For paranoid yoh who stepped into this already ones ;-) lgr.warning("It is unlikely that it was intended to remove all" " files matching %r. Skipping" % filename_) return for f in filenames: try: rmtemp(f) except OSError: # pragma: no cover pass
def _path_(*p): """Given a path in POSIX" notation, regenerate one in native to the env one""" if on_windows: return opj(*map(lambda x: opj(*x.split('/')), p)) else: # Assume that all others as POSIX compliant so nothing to be done return opj(*p)
[docs]def get_timestamp_suffix(time_=None, prefix='-'): """Return a time stamp (full date and time up to second) primarily to be used for generation of log files names """ args = [] if time_ is not None: if isinstance(time_, int): time_ = time.gmtime(time_) args.append(time_) return time.strftime(prefix + TIMESTAMP_FMT, *args)
[docs]def get_logfilename(dspath, cmd='datalad'): """Return a filename to use for logging under a dataset/repository directory would be created if doesn't exist, but dspath must exist and be a directory """ assert(exists(dspath)) assert(isdir(dspath)) ds_logdir = assure_dir(dspath, '.git', 'datalad', 'logs') # TODO: use WEB_META_LOG whenever #789 merged return opj(ds_logdir, 'crawl-%s.log' % get_timestamp_suffix())
[docs]def get_trace(edges, start, end, trace=None): """Return the trace/path to reach a node in a tree. Parameters ---------- edges : sequence(2-tuple) The tree given by a sequence of edges (parent, child) tuples. The nodes can be identified by any value and data type that supports the '==' operation. start : Identifier of the start node. Must be present as a value in the parent location of an edge tuple in order to be found. end : Identifier of the target/end node. Must be present as a value in the child location of an edge tuple in order to be found. trace : list Mostly useful for recursive calls, and used internally. Returns ------- None or list Returns a list with the trace to the target (the starts and the target are not included in the trace, hence if start and end are directly connected an empty list is returned), or None when no trace to the target can be found, or start and end are identical. """ # the term trace is used to avoid confusion with a path in the sense # of a filesystem path, but the analogy fits and nodes can be paths if trace is None: trace = [] if not edges: raise ValueError("no edges given") for cand in edges: cand_super, cand_sub = cand if cand_sub in trace: # only DAGs, skip any cyclic traces continue if trace and cand_super != trace[-1]: # only consider edges that lead off the end of the trace continue if not trace and cand_super != start: # we got nothing yet, and this edges is not matching the start continue if cand_sub == end: return trace # dive into potential subnodes cand_trace = get_trace( edges, start, end, trace + [cand_sub]) if cand_trace: return cand_trace return None
[docs]def get_dataset_root(path): """Return the root of an existent dataset containing a given path The root path is returned in the same absolute or relative form as the input argument. If no associated dataset exists, or the input path doesn't exist, None is returned. """ suffix = '.git' if not isdir(path): path = dirname(path) apath = abspath(path) # while we can still go up while psplit(apath)[1]: if exists(opj(path, suffix)): return path # new test path in the format we got it path = normpath(opj(path, os.pardir)) # no luck, next round apath = abspath(path) return None
# ATM used in datalad_crawler extension, so do not remove yet
[docs]def try_multiple(ntrials, exception, base, f, *args, **kwargs): """Call f multiple times making exponentially growing delay between the calls""" from .dochelpers import exc_str for trial in range(1, ntrials+1): try: return f(*args, **kwargs) except exception as exc: if trial == ntrials: raise # just reraise on the last trial t = base ** trial lgr.warning("Caught %s on trial #%d. Sleeping %f and retrying", exc_str(exc), trial, t) sleep(t)
[docs]@optional_args def try_multiple_dec(f, ntrials=None, duration=0.1, exceptions=None, increment_type=None): """Decorator to try function multiple times. Main purpose is to decorate functions dealing with removal of files/directories and which might need a few seconds to work correctly on Windows which takes its time to release files/directories. Parameters ---------- ntrials: int, optional duration: float, optional Seconds to sleep before retrying. increment_type: {None, 'exponential'} Note that if it is exponential, duration should typically be > 1.0 so it grows with higher power """ from .dochelpers import exc_str if not exceptions: exceptions = (OSError, WindowsError, PermissionError) \ if on_windows else OSError if not ntrials: # Life goes fast on proper systems, no need to delay it much ntrials = 50 if on_windows else 3 assert increment_type in {None, 'exponential'} @wraps(f) def wrapped(*args, **kwargs): t = duration for trial in range(ntrials): try: return f(*args, **kwargs) except exceptions as exc: if increment_type == 'exponential': t = duration ** (trial + 1) lgr.log( 5, "Caught %s on trial #%d. Sleeping %f and retrying", exc_str(exc), trial, t) if trial < ntrials - 1: sleep(t) else: raise return wrapped
@try_multiple_dec def _rmtree(*args, **kwargs): """Just a helper to decorate shutil.rmtree. rmtree defined above does more and ideally should not itself be decorated since a recursive definition and does checks for open files inside etc - might be too runtime expensive """ return shutil.rmtree(*args, **kwargs)
[docs]def slash_join(base, extension): """Join two strings with a '/', avoiding duplicate slashes If any of the strings is None the other is returned as is. """ if extension is None: return base if base is None: return extension return '/'.join( (base.rstrip('/'), extension.lstrip('/')))
[docs]def safe_print(s): """Print with protection against UTF-8 encoding errors""" # A little bit of dance to be able to test this code print_f = getattr(__builtin__, "print") try: print_f(s) except UnicodeEncodeError: # failed to encode so let's do encoding while ignoring errors # to print at least something # explicit `or ascii` since somehow on buildbot it seemed to return None s = s.encode(getattr(sys.stdout, 'encoding', 'ascii') or 'ascii', errors='ignore') \ if hasattr(s, 'encode') else s print_f(s.decode())
# # IO Helpers #
[docs]def open_r_encdetect(fname, readahead=1000): """Return a file object in read mode with auto-detected encoding This is helpful when dealing with files of unknown encoding. Parameters ---------- readahead: int, optional How many bytes to read for guessing the encoding type. If negative - full file will be read """ from chardet import detect import io # read some bytes from the file with open(fname, 'rb') as f: head = enc = detect(head) denc = enc.get('encoding', None) lgr.debug("Auto-detected encoding %s for file %s (confidence: %s)", denc, fname, enc.get('confidence', 'unknown')) return, encoding=denc)
[docs]def read_csv_lines(fname, dialect=None, readahead=16384, **kwargs): """A generator of dict records from a CSV/TSV Automatically guesses the encoding for each record to convert to UTF-8 Parameters ---------- fname: str Filename dialect: str, optional Dialect to specify to csv.reader. If not specified -- guessed from the file, if fails to guess, "excel-tab" is assumed readahead: int, optional How many bytes to read from the file to guess the type **kwargs Passed to `csv.reader` """ import csv if dialect is None: with open(fname) as tsvfile: # add robustness, use a sniffer try: dialect = csv.Sniffer().sniff( except Exception as exc: from .dochelpers import exc_str lgr.warning( 'Could not determine file-format, assuming TSV: %s', exc_str(exc) ) dialect = 'excel-tab' kw = {} if PY2 else dict(encoding='utf-8') with open(fname, 'rb' if PY2 else 'r', **kw) as tsvfile: # doesn't do Unicode; encode temporarily as UTF-8: csv_reader = csv.reader( tsvfile, dialect=dialect, **kwargs ) header = None for row in csv_reader: # decode UTF-8 back to Unicode, cell by cell: row_unicode = map(assure_unicode, row) if header is None: header = list(row_unicode) else: yield dict(zip(header, row_unicode))
[docs]def import_modules(modnames, pkg, msg="Failed to import {module}", log=lgr.debug): """Helper to import a list of modules without failing if N/A Parameters ---------- modnames: list of str List of module names to import pkg: str Package under which to import msg: str, optional Message template for .format() to log at DEBUG level if import fails. Keys {module} and {package} will be provided and ': {exception}' appended log: callable, optional Logger call to use for logging messages """ from importlib import import_module _globals = globals() mods_loaded = [] if pkg and not pkg in sys.modules: # with python 3.5.1 (ok with 3.5.5) somehow kept running into # Failed to import dlsub1: Parent module 'dltestm1' not loaded # while running the test. Preloading pkg resolved the issue import_module(pkg) for modname in modnames: try: _globals[modname] = mod = import_module( '.{}'.format(modname), pkg) mods_loaded.append(mod) except Exception as exc: from datalad.dochelpers import exc_str log((msg + ': {exception}').format( module=modname, package=pkg, exception=exc_str(exc))) return mods_loaded
[docs]def import_module_from_file(modpath, pkg=None, log=lgr.debug): """Import provided module given a path TODO: - RF/make use of it in which has similar logic - join with import_modules above? Parameters ---------- pkg: module, optional If provided, and modpath is under pkg.__path__, relative import will be used """ assert(modpath.endswith('.py')) # for now just for .py files log("Importing %s" % modpath) modname = basename(modpath)[:-3] relmodpath = None if pkg: for pkgpath in pkg.__path__: if path_is_subpath(modpath, pkgpath): # for now relying on having .py extension -- assertion above relmodpath = '.' + relpath(modpath[:-3], pkgpath).replace(sep, '.') break try: if relmodpath: from importlib import import_module mod = import_module(relmodpath, pkg.__name__) else: dirname_ = dirname(modpath) try: sys.path.insert(0, dirname_) mod = __import__(modname, level=0) finally: if dirname_ in sys.path: sys.path.pop(sys.path.index(dirname_)) else: log("Expected path %s to be within sys.path, but it was gone!" % dirname_) except Exception as e: from datalad.dochelpers import exc_str raise RuntimeError( "Failed to import module from %s: %s" % (modpath, exc_str(e))) return mod
[docs]def get_encoding_info(): """Return a dictionary with various encoding/locale information""" import sys, locale from collections import OrderedDict return OrderedDict([ ('default', sys.getdefaultencoding()), ('filesystem', sys.getfilesystemencoding()), ('locale.prefered', locale.getpreferredencoding()), ])
[docs]def get_envvars_info(): from collections import OrderedDict envs = [] for var, val in os.environ.items(): if ( var.startswith('PYTHON') or var.startswith('LC_') or var.startswith('GIT_') or var in ('LANG', 'LANGUAGE', 'PATH') ): envs.append((var, val)) return OrderedDict(envs)
# This class is modified from Snakemake (v5.1.4)
[docs]class SequenceFormatter(string.Formatter): """string.Formatter subclass with special behavior for sequences. This class delegates formatting of individual elements to another formatter object. Non-list objects are formatted by calling the delegate formatter's "format_field" method. List-like objects (list, tuple, set, frozenset) are formatted by formatting each element of the list according to the specified format spec using the delegate formatter and then joining the resulting strings with a separator (space by default). """ def __init__(self, separator=" ", element_formatter=string.Formatter(), *args, **kwargs): self.separator = separator self.element_formatter = element_formatter
[docs] def format_element(self, elem, format_spec): """Format a single element For sequences, this is called once for each element in a sequence. For anything else, it is called on the entire object. It is intended to be overridden in subclases. """ return self.element_formatter.format_field(elem, format_spec)
[docs] def format_field(self, value, format_spec): if isinstance(value, (list, tuple, set, frozenset)): return self.separator.join(self.format_element(v, format_spec) for v in value) else: return self.format_element(value, format_spec)
# TODO: eventually we might want to make use of attr module
[docs]class File(object): """Helper for a file entry in the create_tree/@with_tree It allows to define additional settings for entries """ def __init__(self, name, executable=False): """ Parameters ---------- name : str Name of the file executable: bool, optional Make it executable """ = name self.executable = executable def __str__(self): return
[docs]def create_tree_archive(path, name, load, overwrite=False, archives_leading_dir=True): """Given an archive `name`, create under `path` with specified `load` tree """ from import compress_files dirname = file_basename(name) full_dirname = op.join(path, dirname) os.makedirs(full_dirname) create_tree(full_dirname, load, archives_leading_dir=archives_leading_dir) # create archive if archives_leading_dir: compress_files([dirname], name, path=path, overwrite=overwrite) else: compress_files(list(map(op.basename, glob.glob(opj(full_dirname, '*')))), opj(op.pardir, name), path=op.join(path, dirname), overwrite=overwrite) # remove original tree rmtree(full_dirname)
[docs]def create_tree(path, tree, archives_leading_dir=True, remove_existing=False): """Given a list of tuples (name, load) create such a tree if load is a tuple itself -- that would create either a subtree or an archive with that content and place it into the tree if name ends with .tar.gz """ lgr.log(5, "Creating a tree under %s", path) if not op.exists(path): os.makedirs(path) if isinstance(tree, dict): tree = tree.items() for file_, load in tree: if isinstance(file_, File): executable = file_.executable name = else: executable = False name = file_ full_name = op.join(path, name) if remove_existing and op.lexists(full_name): rmtree(full_name, chmod_files=True) if isinstance(load, (tuple, list, dict)): if name.endswith('.tar.gz') or name.endswith('.tar') or name.endswith('.zip'): create_tree_archive( path, name, load, archives_leading_dir=archives_leading_dir) else: create_tree( full_name, load, archives_leading_dir=archives_leading_dir, remove_existing=remove_existing) else: open_func = open if full_name.endswith('.gz'): open_func = with open_func(full_name, "wb") as f: f.write(assure_bytes(load, 'utf-8')) if executable: os.chmod(full_name, os.stat(full_name).st_mode | stat.S_IEXEC)
[docs]def get_suggestions_msg(values, known, sep="\n "): """Return a formatted string with suggestions for values given the known ones """ import difflib suggestions = [] for value in assure_list(values): # might not want to do it if we change presentation below suggestions += difflib.get_close_matches(value, known) suggestions = unique(suggestions) msg = "Did you mean any of these?" if suggestions: if '\n' in sep: # if separator includes new line - we add entire separator right away msg += sep else: msg += ' ' return msg + "%s\n" % sep.join(suggestions) return ''
[docs]def bytes2human(n, format='%(value).1f %(symbol)sB'): """ Convert n bytes into a human readable string based on format. symbols can be either "customary", "customary_ext", "iec" or "iec_ext", see: >>> from datalad.utils import bytes2human >>> bytes2human(1) '1.0 B' >>> bytes2human(1024) '1.0 KB' >>> bytes2human(1048576) '1.0 MB' >>> bytes2human(1099511627776127398123789121) '909.5 YB' >>> bytes2human(10000, "%(value).1f %(symbol)s/sec") '9.8 K/sec' >>> # precision can be adjusted by playing with %f operator >>> bytes2human(10000, format="%(value).5f %(symbol)s") '9.76562 K' Taken from: and subsequently simplified Original Author: Giampaolo Rodola' <g.rodola [AT] gmail [DOT] com> License: MIT """ n = int(n) if n < 0: raise ValueError("n < 0") symbols = ('', 'K', 'M', 'G', 'T', 'P', 'E', 'Z', 'Y') prefix = {} for i, s in enumerate(symbols[1:]): prefix[s] = 1 << (i + 1) * 10 for symbol in reversed(symbols[1:]): if n >= prefix[symbol]: value = float(n) / prefix[symbol] return format % locals() return format % dict(symbol=symbols[0], value=n)
lgr.log(5, "Done importing datalad.utils")