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# ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import os
import pathlib
import shutil
import distutils
import tempfile
import weakref
from qiime2.core.util import set_permissions, USER_GROUP_RWX
_ConcretePath = type(pathlib.Path())
def _party_parrot(self, *args):
raise TypeError("Cannot mutate %r." % self)
class OwnedPath(_ConcretePath):
def __new__(cls, *args, **kwargs):
self = super().__new__(cls, *args, **kwargs)
self._user_owned = True
return self
def _copy_dir_or_file(self, other):
if self.is_dir():
return distutils.dir_util.copy_tree(str(self), str(other))
else:
return shutil.copy(str(self), str(other))
def _destruct(self):
if self.is_dir():
distutils.dir_util.remove_tree(str(self))
else:
self.unlink()
def _move_or_copy(self, other):
if self._user_owned:
return self._copy_dir_or_file(other)
else:
# Certain networked filesystems will experience a race
# condition on `rename`, so fall back to copying.
try:
return _ConcretePath.rename(self, other)
except (FileExistsError, OSError) as e:
# OSError errno 18 is cross device link, if we have this error
# we can solve it by copying. If we have a different OSError we
# still want to explode. FileExistsErrors are apparently
# instances of OSError, so we also make sure we don't have one
# of them when we explode
if isinstance(e, OSError) and e.errno != 18 and \
not isinstance(e, FileExistsError):
raise e
copied = self._copy_dir_or_file(other)
self._destruct()
return copied
class InPath(OwnedPath):
def __new__(cls, path):
self = super().__new__(cls, path)
self.__backing_path = path
if hasattr(path, '_user_owned'):
self._user_owned = path._user_owned
return self
chmod = lchmod = rename = replace = rmdir = symlink_to = touch = unlink = \
write_bytes = write_text = _party_parrot
def open(self, mode='r', buffering=-1, encoding=None, errors=None,
newline=None):
if 'w' in mode or ' ' in mode or 'a' in mode:
_party_parrot(self)
return super().open(mode=mode, buffering=buffering, encoding=encoding,
errors=errors, newline=newline)
class OutPath(OwnedPath):
@classmethod
def _destruct(cls, path):
if not os.path.exists(path):
return
if os.path.isdir(path):
shutil.rmtree(path)
else:
os.unlink(path)
def __new__(cls, dir=False, **kwargs):
"""
Create a tempfile, return pathlib.Path reference to it.
"""
if dir:
name = tempfile.mkdtemp(**kwargs)
else:
fd, name = tempfile.mkstemp(**kwargs)
# fd is now assigned to our process table, but we don't need to do
# anything with the file. We will call `open` on the `name` later
# producing a different file descriptor, so close this one to
# prevent a resource leak.
os.close(fd)
obj = super().__new__(cls, name)
obj._destructor = weakref.finalize(obj, cls._destruct, str(obj))
return obj
def __exit__(self, t, v, tb):
self._destructor()
class InternalDirectory(_ConcretePath):
DEFAULT_PREFIX = 'qiime2-'
@classmethod
def _destruct(cls, path):
"""DO NOT USE DIRECTLY, use `_destructor()` instead"""
if os.path.exists(path):
set_permissions(path, None, USER_GROUP_RWX)
shutil.rmtree(path)
@classmethod
def __new(cls, *args):
self = super().__new__(cls, *args)
self._destructor = weakref.finalize(self, self._destruct, str(self))
return self
def __new__(cls, *args, prefix=None):
if args and prefix is not None:
raise TypeError("Cannot pass a path and a prefix at the same time")
elif args:
# This happens when the base-class's __reduce__ method is invoked
# for pickling.
return cls.__new(*args)
else:
if prefix is None:
prefix = cls.DEFAULT_PREFIX
elif not prefix.startswith(cls.DEFAULT_PREFIX):
prefix = cls.DEFAULT_PREFIX prefix
# TODO: normalize when temp-directories are configurable
path = tempfile.mkdtemp(prefix=prefix)
return cls.__new(path)
def __truediv__(self, path):
# We don't want to create self-destructing paths when using the join
# operator
return _ConcretePath(str(self), path)
def __rtruediv__(self, path):
# Same reasoning as truediv
return _ConcretePath(path, str(self))
def rename(self, path):
# We don't want to rename and lose the target right away.
# This overrides post python3.8 behavior.
_ConcretePath(str(self)).rename(path)
def replace(self, path):
# Same reasoning as replace
_ConcretePath(str(self)).replace(path)
class ArchivePath(InternalDirectory):
DEFAULT_PREFIX = 'qiime2-archive-'
class ProvenancePath(InternalDirectory):
DEFAULT_PREFIX = 'qiime2-provenance-'
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