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"""
Redirect calls to open, etc. to a virtual file system.
Use this to mount a zip file as a file system, and then all subsequent calls
to chdir, open, etc. will reference files in the zip file instead of the disk.
This will only work for packages which do all their I/O in python, and not
those which use direct calls to the C library, so for example, it will not
work with h5py. XML parsing from a zip file is also unlikely to work since
expat uses the C library directly for parsing.
Usage::
# Do this before importing any other modules! It sets up hooks for
# redirecting filesystem access even if the module imports the symbol
# directly as "from os import getcwd".
import vfs
vfs.vfs_init()
...
with vfs.ZipFS('data.zip'):
data = np.loadtxt('file1.dat')
Filesystems available:
* `RealFS` - uses the builtin python functions to access the O/S.
* `ZipFS` - opens a zip file as the filesystem root.
Calls redirected::
__builtin__.open (python 2 only)
builtins.open (python 2 and 3)
io.open (python 2 and 3)
os, nt, posix:
chdir, getcwd, listdir
os.path, ntpath, posixpath:
exists, isfile, isir, abspath, realpath
You can also use the file systems directly without using the `vfs_init`
hook or the with statement. Just call `fs.chdir`, etc. on the file system
object.
*file* in python 2.x is a type as well as constructor, so a simple redirect
to a replacement constructor will not work. Don't try to support it since
it is gone in python 3.
Works with numpy.loadtxt and pandas parsers.
For pandas, either need to specify *engine="python"* or pass an open call
to the reader; if you just pass a filename, then it will try opening it
with the libc open function and fail. Could potentially monkeypatch
pandas to pre-open the file.
"""
import sys
import os
import os.path
import io
from functools import wraps
try:
import __builtin__
from __builtin__ import open as _py2_open
except ImportError:
__builtin__ = _py2_open = None
try:
import builtins
except ImportError:
builtins = None
try:
from pathlib import PurePath
except ImportError:
class PurePath:
pass
# Sphinx hack: in order to avoid having sphinx pick up the docstrings for the
# builtin functions (chdir and listdir don't format properly), simply suppress
# all classes for the module.
__all__ = []
# TODO: restructure according to pathlib interface
# Looking at pathlib, it already provides methods close to what we implement
# for our virtual file system. By following the pathlib interface directly,
# then any code that is set up to use pathlib can use our virtual file systems
# without change (in particular, without monkeypatching python builtins).
# for functions that work for read-only filesystems, use *fn
# for functions implemented as python, use -fn
#
# os functions
# *chdir, *getcwd, *listdir, rmdir, mkdir, chroot
# *open, *stat, *access, rename, link, unlink, remove chmod, chown, chflags
# *getcwdb, *getcwdu # bytes getcwd (py3), unicode getcwd (py2)
# *scandir
# -makedirs # uses exists, split, mkdir
# -removedirs # uses split, rmdir
# -walk # uses islink, join, isdir, listdir
# -glob.glob # uses lexists, isdir, join, scandir
# symbolic link functions
# *readlink, *lstat, symlink, lchflags, lchmod, lchown
# *os.path.lexists
# os.path functions
# *exists, *isfile, *isdir
# *get[acm]time, *getsize
# samefile # uses stat, samestat
# samestat # uses filestat.dev and filestat.inode; compares device/inode
# -isabs # uses str; returns s.startswith('/')
# -normpath # uses str; pure path manipulation
# -abspath # uses isabs, normpath, getcwd/getcwdu
# -realpath # uses isabs, split, join, islink, readlink
# -renames # uses exists, split, rename, makedirs, removedirs
# -walk # uses listdir, lstat; deprecated in favour of os.walk
# os/os.path constants
# curdir, pardir, sep, pathsep, defpath, extsep, altsep, linesep
# file descriptor operations in os
# fchdir, fchmod, fchown, fdopen, close, fstat, fstatvfs, fpathconf,
# lseek, read, dup, dup2, errno, error, closerange, isatty, openpty,
# mknod
# Protect against reload(vfs). Assume that if the symbol is already a
# wrapped symbol that we want to retrieve the original unwrapped symbol
# rather than our wrapper. Additionally, assume nobody else is foolish
# enough to be wrapping such low-level symbols...
def _unwrap(fn):
return getattr(fn, "__wrapped__", fn)
_py2_open = _unwrap(_py2_open)
_py3_open = _unwrap(io.open)
_chdir = _unwrap(os.chdir)
_getcwd = _unwrap(os.getcwd)
_exists = _unwrap(os.path.exists)
_isfile = _unwrap(os.path.isfile)
_isdir = _unwrap(os.path.isdir)
_listdir = _unwrap(os.listdir)
# TODO: maybe use builtin versions?
_abspath = _unwrap(os.path.abspath)
_realpath = _unwrap(os.path.realpath)
class RealFS(object):
def __enter__(self):
pushfs(RealFS)
def __exit__(self, *args, **kw):
popfs()
open = _py3_open
py2_open = _py2_open
getcwd = _getcwd
chdir = _chdir
listdir = _listdir
abspath = _abspath
realpath = _realpath
isfile = _isfile
isdir = _isdir
exists = _exists
class ZipFS(object):
"""
Opens a zip file as the root file system.
"""
def __init__(self, path):
import zipfile
# TODO: can we open a zip within a zip?
# Apparently yes, but only if we read the file into a byte stream and
# then work from that file. See the following stackoverflow answer:
# https://stackoverflow.com/questions/12025469/how-to-read-from-a-zip-file-within-zip-file-in-python
self._path = _realpath(path)
self._wd = "/"
self._zip = zipfile.ZipFile(path)
def __enter__(self):
pushfs(self)
return self._zip
def __exit__(self, *args, **kw):
popfs()
def open(self, file, mode="r", buffering=-1, encoding=None, errors=None, newline=None, **kw):
# abspath handles pathlib
# Note: python 3 zipfile only supports mode rb; to get unicode
# decoding, need to wrap the binary stream in a text I/O wrapper.
zipmode = "r"
with RealFS():
fd = self._zip.open(self.abspath(file)[1:], mode=zipmode)
if "b" in mode:
return fd
else:
return io.TextIOWrapper(fd, encoding=encoding, errors=errors, newline=newline)
def py2_open(self, name, mode="r", buffering=-1):
# abspath handles pathlib
# Note: python 2 zipfile supports modes r, rU, and U, but not rb
zipmode = "r" if mode == "rb" else mode
with RealFS():
fd = self._zip.open(self.abspath(name)[1:], mode=zipmode)
return fd
def chdir(self, path):
# abspath handles pathlib
if self.isdir(path):
self._wd = self.abspath(path) + "/"
def _iter_dir(self, path=None):
# TODO: turn this into a scandir interface
# abspath handles pathlib
path = self._wd if path is None else self.abspath(path)
path = path[1:]
n = len(path)
seen = {}
for f in self._zip.filelist:
if not f.filename.startswith(path):
# it is not part of the tree
continue
parts = f.filename.split("/")
if len(parts) == 1:
# it is a leaf so report it
yield parts[0]
elif parts[0] not in seen:
# it is a directory, so only report it if it has not already
# been reported
seen.add(parts[0])
yield parts[0]
def listdir(self, path=None):
# abspath handles pathlib
return [f for f in self._iter_dir(path)]
def abspath(self, path):
if isinstance(path, PurePath):
path = path.as_posix()
if hasattr(path, "decode"): # CRUFT: python 2
path = path.decode()
if path[0] != "/":
path = "/".join((self._wd[:-1], path))
return os.path.normpath(path)
def realpath(self, filename):
# abspath handles pathlib
return os.path.join(self._path, self.abspath(filename))
def isfile(self, path):
# abspath handles pathlib
path = self.abspath(path)[1:]
return any(path == f.filename for f in self._zip.filelist)
def isdir(self, s):
# abspath handles pathlib
path = self.abspath(s)[1:] + "/"
for f in self._zip.filelist:
if f.filename.startswith(path):
return True
return False
def exists(self, path):
# abspath handles pathlib
return self.isfile(path) or self.isdir(path)
FS = RealFS
FS_STACK = [] # type: List[RealFS]
def pushfs(fs):
global FS
FS_STACK.append(FS)
FS = fs
def popfs():
global FS
FS = FS_STACK.pop()
# Note: We need fs redirection functions as bound methods since pathlib uses
# them as class attributes. The usual filesystem methods are all builtin
# functions so they act as static methods when used as part of a class
# definition. However, when python functions are used as class attributes
# they get turned into bound methods when an object is created with self
# as the first parameter. But if the class attribute is already a bound method
# then it is left alone when the object is created. We still get the extra
# self parameter, but we get it whether we access it as a class attribute
# or as an object attribute so it is easy to ignore.
class VFS(object):
if _py3_open is not None:
@wraps(_py3_open)
def fs_py3_open(self, *args, **kw):
return FS.open(*args, **kw)
if _py2_open is not None:
@wraps(_py2_open)
def fs_py2_open(self, *args, **kw):
return FS.py2_open(*args, **kw)
@wraps(_chdir)
def fs_chdir(self, *args, **kw):
return FS.chdir(*args, **kw)
@wraps(_getcwd)
def fs_getcwd(self, *args, **kw):
return FS.getcwd(*args, **kw)
@wraps(_listdir)
def fs_listdir(self, *args, **kw):
return FS.listdir(*args, **kw)
@wraps(_exists)
def fs_exists(self, *args, **kw):
return FS.exists(*args)
@wraps(_isfile)
def fs_isfile(self, *args, **kw):
return FS.isfile(*args, **kw)
@wraps(_isdir)
def fs_isdir(self, *args, **kw):
return FS.isdir(*args, **kw)
@wraps(_abspath)
def fs_abspath(self, *args, **kw):
return FS.abspath(*args, **kw)
@wraps(_realpath)
def fs_realpath(self, *args, **kw):
return FS.realpath(*args, **kw)
vfs = VFS()
def vfs_init():
"""
Call this very early in your program so that various filesystem functions
will be redirected even if they are expressed as "from module import fn"
"""
if __builtin__ is not None:
__builtin__.open = vfs.fs_py2_open
if builtins is not None:
builtins.open = vfs.fs_py3_open
io.open = vfs.fs_py3_open
os.chdir = vfs.fs_chdir
os.getcwd = vfs.fs_getcwd
os.listdir = vfs.fs_listdir
os.path.abspath = vfs.fs_abspath
os.path.realpath = vfs.fs_realpath
os.path.exists = vfs.fs_exists
os.path.isfile = vfs.fs_isfile
os.path.isdir = vfs.fs_isdir
try:
import nt, ntpath
nt.chdir = vfs.fs_chdir
nt.listdir = vfs.fs_listdir
nt.getcwd = vfs.fs_getcwd
ntpath.abspath = vfs.fs_abspath
ntpath.realpath = vfs.fs_realpath
ntpath.exists = vfs.fs_exists
ntpath.isfile = vfs.fs_isfile
ntpath.isdir = vfs.fs_isdir
except ImportError:
pass
try:
import posix, posixpath
posix.chdir = vfs.fs_chdir
posix.listdir = vfs.fs_listdir
posix.getcwd = vfs.fs_getcwd
posixpath.abspath = vfs.fs_abspath
posixpath.realpath = vfs.fs_realpath
posixpath.exists = vfs.fs_exists
posixpath.isfile = vfs.fs_isfile
posixpath.isdir = vfs.fs_isdir
except ImportError:
pass
# Pathlib may be imported really early. Make sure it sees the vfs.
# TODO: with reload some isinstance tests may fail --- monkeypatch instead?
# Should be just an update to the members of pathlib._NormalAccessor.
# With reload, os.PathLike.register(PurePath) is being called twice but that
# shouldn't be a problem, especially because PurePath will have changed.
try:
import pathlib
from importlib import reload
reload(pathlib)
except ImportError:
pass
# CRUFT: use old wrappers for python 2 since new wrappers don't seem to work
if sys.version_info[0] == 2:
class RealFS(object):
def __enter__(self):
pushfs(self)
def __exit__(self, *args, **kw):
popfs()
def open(self, *args, **kw):
return _py3_open(*args, **kw)
def py2_open(self, *args, **kw):
return _py2_open(*args, **kw)
def getcwd(self):
return _getcwd()
def chdir(self, path):
return _chdir(path)
def listdir(self, path=None):
return _listdir(path) if path is not None else _listdir()
def abspath(self, path):
return _abspath(path)
def realpath(self, path):
return _realpath(path)
def isfile(self, path):
return _isfile(path)
def isdir(self, path):
return _isdir(path)
def exists(self, path):
return _exists(path)
if _py3_open is not None:
@wraps(_py3_open)
def fs_py3_open(*args, **kw):
return FS.open(*args, **kw)
if _py2_open is not None:
@wraps(_py2_open)
def fs_py2_open(*args, **kw):
return FS.py2_open(*args, **kw)
@wraps(_chdir)
def fs_chdir(*args, **kw):
return FS.chdir(*args, **kw)
@wraps(_getcwd)
def fs_getcwd(*args, **kw):
return FS.getcwd(*args, **kw)
@wraps(_listdir)
def fs_listdir(*args, **kw):
return FS.listdir(*args, **kw)
@wraps(_exists)
def fs_exists(*args, **kw):
return FS.exists(*args)
@wraps(_isfile)
def fs_isfile(*args, **kw):
return FS.isfile(*args, **kw)
@wraps(_isdir)
def fs_isdir(*args, **kw):
return FS.isdir(*args, **kw)
@wraps(_abspath)
def fs_abspath(*args, **kw):
return FS.abspath(*args, **kw)
@wraps(_realpath)
def fs_realpath(*args, **kw):
return FS.realpath(*args, **kw)
def vfs_init():
"""
Call this very early in your program so that various filesystem functions
will be redirected even if they are expressed as "from module import fn"
"""
global FS
FS = RealFS()
if __builtin__ is not None:
__builtin__.open = fs_py2_open
if builtins is not None:
builtins.open = fs_py3_open
io.open = fs_py3_open
os.chdir = fs_chdir
os.getcwd = fs_getcwd
os.listdir = fs_listdir
os.path.abspath = fs_abspath
os.path.realpath = fs_realpath
os.path.exists = fs_exists
os.path.isfile = fs_isfile
os.path.isdir = fs_isdir
try:
import nt, ntpath
nt.chdir = fs_chdir
nt.listdir = fs_listdir
nt.getcwd = fs_getcwd
ntpath.abspath = fs_abspath
ntpath.realpath = fs_realpath
ntpath.exists = fs_exists
ntpath.isfile = fs_isfile
ntpath.isdir = fs_isdir
except ImportError:
pass
try:
import posix, posixpath
posix.chdir = fs_chdir
posix.listdir = fs_listdir
posix.getcwd = fs_getcwd
posixpath.abspath = fs_abspath
posixpath.realpath = fs_realpath
posixpath.exists = fs_exists
posixpath.isfile = fs_isfile
posixpath.isdir = fs_isdir
except ImportError:
pass
# Pathlib may be imported really early. Make sure it sees the vfs.
# TODO: with reload some isinstance tests may fail --- monkeypatch instead?
# Should be just an update to the members of pathlib._NormalAccessor.
# With reload, os.PathLike.register(PurePath) is being called twice but that
# shouldn't be a problem, especially because PurePath will have changed.
try:
import pathlib
from importlib import reload
reload(pathlib)
except ImportError:
pass
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