gzip - Unzipping part of a .gz file using python

Question

So here's the problem. I have sample.gz file which is roughly 60KB in size. I want to decompress the first 2000 bytes of this file. I am running into CRC check failed error, I guess because the gzip CRC field appears at the end of file, and it requires the entire gzipped file to decompress. Is there a way to get around this? I don't care about the CRC check. Even if I fail to decompress because of bad CRC, that is OK. Is there a way to get around this and unzip partial .gz files?

The code I have so far is

import gzip
import time
import StringIO

file = open('sample.gz', 'rb')
mybuf = MyBuffer(file)
mybuf = StringIO.StringIO(file.read(2000))
f = gzip.GzipFile(fileobj=mybuf)
data = f.read()
print data

The error encountered is

File "gunzip.py", line 27, in ?
    data = f.read()
File "/usr/local/lib/python2.4/gzip.py", line 218, in read
  self._read(readsize)
File "/usr/local/lib/python2.4/gzip.py", line 273, in _read
  self._read_eof()
File "/usr/local/lib/python2.4/gzip.py", line 309, in _read_eof
  raise IOError, "CRC check failed"
IOError: CRC check failed

Also is there any way to use zlib module to do this and ignore the gzip headers?

Answer 1

The issue with the gzip module is not that it can't decompress the partial file, the error occurs only at the end when it tries to verify the checksum of the decompressed content. (The original checksum is stored at the end of the compressed file so the verification will never, ever work with a partial file.)

The key is to trick gzip into skipping the verification. The answer by caesar0301 does this by modifying the gzip source code, but it's not necessary to go that far, simple monkey patching will do. I wrote this context manager to temporarily replace gzip.GzipFile._read_eof while I decompress the partial file:

import contextlib

@contextlib.contextmanager
def patch_gzip_for_partial():
    """
    Context manager that replaces gzip.GzipFile._read_eof with a no-op.

    This is useful when decompressing partial files, something that won't
    work if GzipFile does it's checksum comparison.

    """
    _read_eof = gzip.GzipFile._read_eof
    gzip.GzipFile._read_eof = lambda *args, **kwargs: None
    yield
    gzip.GzipFile._read_eof = _read_eof

An example usage:

from cStringIO import StringIO

with patch_gzip_for_partial():
    decompressed = gzip.GzipFile(StringIO(compressed)).read()