New submission from Ruben Vorderman <r.h.p.vorder...@lumc.nl>:
Please consider the following code snippet:
import gzip
import sys
with gzip.open(sys.argv[1], "rt") as in_file_h:
with gzip.open(sys.argv[2], "wt", compresslevel=1) as out_file_h:
for line in in_file_h:
# Do processing on line here
modified_line = line
# End processing
out_file_h.write(modified_line)
This is very slow, due to write being called for every line. This is the
current implementation of write:
https://github.com/python/cpython/blob/c379bc5ec9012cf66424ef3d80612cf13ec51006/Lib/gzip.py#L272
It:
- Checks if the file is not closed
- Checks if the correct mode is set
- Checks if the file is not closed (again, but in a different way)
- Checks if the data is bytes, bytearray or something that supports the buffer
protocol
- Gets the length
- Compresses the data
- updates the size and offset
- updates the checksum
Doing this for every line written is very costly and creates a lot of overhead
in Python calls. We spent a lot of time in Python and a lot less in the fast C
zlib code that does the actual compression.
This problem is already solved on the read side. A _GzipReader object is used
for reading. This is put in an io.BufferedReader which is used as the
underlying buffer for GzipFile.read. This way, lines are read quite fast from
a GzipFile without the checksum etc. being updated on every line read.
A similar solution should be written for write.
I volunteer (I have done some other work on gzip.py already), although I cannot
give an ETA at this time.
----------
messages: 403289
nosy: rhpvorderman
priority: normal
severity: normal
status: open
title: GzipFile.write should be buffered
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Python tracker <rep...@bugs.python.org>
<https://bugs.python.org/issue45387>
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