"""Utilities for fast persistence of big data, with optional compression."""
# Author: Gael Varoquaux <gael dot varoquaux at normalesup dot org>
# Copyright (c) 2009 Gael Varoquaux
# License: BSD Style, 3 clauses.
import pickle
import io
import warnings
import contextlib
from contextlib import closing
from ._compat import PY3_OR_LATER, PY27
from .compressor import _ZFILE_PREFIX
from .compressor import _COMPRESSORS
if PY3_OR_LATER:
Unpickler = pickle._Unpickler
Pickler = pickle._Pickler
xrange = range
else:
Unpickler = pickle.Unpickler
Pickler = pickle.Pickler
try:
import numpy as np
except ImportError:
np = None
try:
# The python standard library can be built without bz2 so we make bz2
# usage optional.
# see https://github.com/scikit-learn/scikit-learn/issues/7526 for more
# details.
import bz2
except ImportError:
bz2 = None
# Buffer size used in io.BufferedReader and io.BufferedWriter
_IO_BUFFER_SIZE = 1024 ** 2
def _is_raw_file(fileobj):
"""Check if fileobj is a raw file object, e.g created with open."""
if PY3_OR_LATER:
fileobj = getattr(fileobj, 'raw', fileobj)
return isinstance(fileobj, io.FileIO)
else:
return isinstance(fileobj, file) # noqa
def _get_prefixes_max_len():
# Compute the max prefix len of registered compressors.
prefixes = [len(compressor.prefix) for compressor in _COMPRESSORS.values()]
prefixes += [len(_ZFILE_PREFIX)]
return max(prefixes)
###############################################################################
# Cache file utilities
def _detect_compressor(fileobj):
"""Return the compressor matching fileobj.
Parameters
----------
fileobj: file object
Returns
-------
str in {'zlib', 'gzip', 'bz2', 'lzma', 'xz', 'compat', 'not-compressed'}
"""
# Read the magic number in the first bytes of the file.
max_prefix_len = _get_prefixes_max_len()
if hasattr(fileobj, 'peek'):
# Peek allows to read those bytes without moving the cursor in the
# file whic.
first_bytes = fileobj.peek(max_prefix_len)
else:
# Fallback to seek if the fileobject is not peekable.
first_bytes = fileobj.read(max_prefix_len)
fileobj.seek(0)
if first_bytes.startswith(_ZFILE_PREFIX):
return "compat"
else:
for name, compressor in _COMPRESSORS.items():
if first_bytes.startswith(compressor.prefix):
return name
return "not-compressed"
def _buffered_read_file(fobj):
"""Return a buffered version of a read file object."""
if PY27 and bz2 is not None and isinstance(fobj, bz2.BZ2File):
# Python 2.7 doesn't work with BZ2File through a buffer: "no
# attribute 'readable'" error.
return fobj
else:
return io.BufferedReader(fobj, buffer_size=_IO_BUFFER_SIZE)
def _buffered_write_file(fobj):
"""Return a buffered version of a write file object."""
if PY27 and bz2 is not None and isinstance(fobj, bz2.BZ2File):
# Python 2.7 doesn't work with BZ2File through a buffer: no attribute
# 'writable'.
# BZ2File doesn't implement the file object context manager in python 2
# so we wrap the fileobj using `closing`.
return closing(fobj)
else:
return io.BufferedWriter(fobj, buffer_size=_IO_BUFFER_SIZE)
@contextlib.contextmanager
def _read_fileobject(fileobj, filename, mmap_mode=None):
"""Utility function opening the right fileobject from a filename.
The magic number is used to choose between the type of file object to open:
* regular file object (default)
* zlib file object
* gzip file object
* bz2 file object
* lzma file object (for xz and lzma compressor)
Parameters
----------
fileobj: file object
compressor: str in {'zlib', 'gzip', 'bz2', 'lzma', 'xz', 'compat',
'not-compressed'}
filename: str
filename path corresponding to the fileobj parameter.
mmap_mode: str
memory map mode that should be used to open the pickle file. This
parameter is useful to verify that the user is not trying to one with
compression. Default: None.
Returns
-------
a file like object
"""
# Detect if the fileobj contains compressed data.
compressor = _detect_compressor(fileobj)
if compressor == 'compat':
# Compatibility with old pickle mode: simply return the input
# filename "as-is" and let the compatibility function be called by the
# caller.
warnings.warn("The file '%s' has been generated with a joblib "
"version less than 0.10. "
"Please regenerate this pickle file." % filename,
DeprecationWarning, stacklevel=2)
yield filename
else:
if compressor in _COMPRESSORS:
# based on the compressor detected in the file, we open the
# correct decompressor file object, wrapped in a buffer.
compressor_wrapper = _COMPRESSORS[compressor]
inst = compressor_wrapper.decompressor_file(fileobj)
fileobj = _buffered_read_file(inst)
# Checking if incompatible load parameters with the type of file:
# mmap_mode cannot be used with compressed file or in memory buffers
# such as io.BytesIO.
if mmap_mode is not None:
if isinstance(fileobj, io.BytesIO):
warnings.warn('In memory persistence is not compatible with '
'mmap_mode "%(mmap_mode)s" flag passed. '
'mmap_mode option will be ignored.'
% locals(), stacklevel=2)
elif compressor != 'not-compressed':
warnings.warn('mmap_mode "%(mmap_mode)s" is not compatible '
'with compressed file %(filename)s. '
'"%(mmap_mode)s" flag will be ignored.'
% locals(), stacklevel=2)
elif not _is_raw_file(fileobj):
warnings.warn('"%(fileobj)r" is not a raw file, mmap_mode '
'"%(mmap_mode)s" flag will be ignored.'
% locals(), stacklevel=2)
yield fileobj
def _write_fileobject(filename, compress=("zlib", 3)):
"""Return the right compressor file object in write mode."""
compressmethod = compress[0]
compresslevel = compress[1]
if compressmethod in _COMPRESSORS.keys():
file_instance = _COMPRESSORS[compressmethod].compressor_file(
filename, compresslevel=compresslevel)
return _buffered_write_file(file_instance)
else:
file_instance = _COMPRESSORS['zlib'].compressor_file(
filename, compresslevel=compresslevel)
return _buffered_write_file(file_instance)
# Utility functions/variables from numpy required for writing arrays.
# We need at least the functions introduced in version 1.9 of numpy. Here,
# we use the ones from numpy 1.10.2.
BUFFER_SIZE = 2 ** 18 # size of buffer for reading npz files in bytes
def _read_bytes(fp, size, error_template="ran out of data"):
"""Read from file-like object until size bytes are read.
Raises ValueError if not EOF is encountered before size bytes are read.
Non-blocking objects only supported if they derive from io objects.
Required as e.g. ZipExtFile in python 2.6 can return less data than
requested.
This function was taken from numpy/lib/format.py in version 1.10.2.
Parameters
----------
fp: file-like object
size: int
error_template: str
Returns
-------
a bytes object
The data read in bytes.
"""
data = bytes()
while True:
# io files (default in python3) return None or raise on
# would-block, python2 file will truncate, probably nothing can be
# done about that. note that regular files can't be non-blocking
try:
r = fp.read(size - len(data))
data += r
if len(r) == 0 or len(data) == size:
break
except io.BlockingIOError:
pass
if len(data) != size:
msg = "EOF: reading %s, expected %d bytes got %d"
raise ValueError(msg % (error_template, size, len(data)))
else:
return data