[Tutor] Trying to parse a HUGE(1gb) xml file in python

[ashish makani]

Hi Python Tutor folks

This is a rather long post, but i wanted to include all the details &
everything i have tried so far myself, so please bear with me & read the
entire boringly long post.

Goal : I am trying to parse a ginormous ( ~ 1gb) xml file.

I am looking for a specific element..there are several 10s/100s occurrences
of that element in the 1gb file.

I need to detect them & then for each 1, i need to copy all the content b/w
the element's start & end tags & create a smaller xml


0. I am a python & xml n00b, s& have been relying on the excellent beginner
book DIP(Dive_Into_Python3 by MP(Mark Pilgrim).... Mark , if u are readng
this, you are AWESOME & so is your witty & humorous writing style)

My hardware setup : I have a win7 pro box with 8gb of RAM & intel core2 quad
cpuq9400.
On this i am running sun virtualbox(3.2.12), with ubuntu 10.10(maverick) as
guest os, with 23gb disk space & 2gb(2048mb) ram, assigned to the guest
ubuntu os.

1. Almost all exmaples pf parsing xml in python, i have seen, start off with
these 4 lines of code.

import xml.etree.ElementTree as etree
tree = etree.parse('*path_to_ginormous_xml*')
root = tree.getroot()  #my huge xml has 1 root at the top level
print root

2. In the 2nd line of code above, as Mark explains in DIP, the parse
function builds & returns a tree object, in-memory(RAM), which represents
the entire document.
I tried this code, which works fine for a small ( ~ 1MB), but when i run
this simple 4 line py code in a terminal for my HUGE target file (1GB),
nothing happens.
In a separate terminal, i run the top command, & i can see a python process,
with memory (the VIRT column) increasing from 100MB , all the way upto
2100MB.

I am guessing, as this happens (over the course of 20-30 mins), the tree
representing is being slowly built in memory, but even after 30-40 mins,
nothing happens.
I dont get an error, seg fault or out_of_memory exception.

3. I also tried using lxml, but an lxml tree is much more expensive, as it
retains more info about a node's context, including references to it's
parent.

[http://www.ibm.com/developerworks/xml/library/x-hiperfparse/]

When i ran the same 4line code above, but with lxml's elementree ( using the
import below in line1of the code above)
import lxml.etree as lxml_etree

i can see the memory consumption of the python process(which is running the
code) shoot upto ~ 2700mb & then, python(or the os ?) kills the process as
it nears the total system memory(2gb)

I ran the code from 1 terminal window (screenshot :
http://imgur.com/ozLkB.png)
& ran top from another terminal (http://imgur.com/HAoHA.png)

4. I then investigated some streaming libraries, but am confused - there is
SAX[http://en.wikipedia.org/wiki/Simple_API_for_XML] , the iterparse
interface[http://effbot.org/zone/element-iterparse.htm], & several otehr
options ( minidom)

Which one is the best for my situation ?

Should i instead just open the file, & use reg ex to look for the element i
need ?


Any & all code_snippets/wisdom/thoughts/ideas/suggestions/feedback/comments/
of the Python tutor community would be greatly appreciated.
Plz feel free to email me directly too.

thanks a ton

cheers
ashish

email :
ashish.makani
domain:gmail.com

p.s.
Other useful links on xml parsing in python
0. http://diveintopython3.org/xml.html
1.
http://stackoverflow.com/questions/1513592/python-is-there-an-xml-parser-implemented-as-a-generator
2. http://codespeak.net/lxml/tutorial.html
3.
https://groups.google.com/forum/?hl=en&lnk=gst&q=parsing+a+huge+xml#!topic/comp.lang.python/CMgToEnjZBk
4. http://www.ibm.com/developerworks/xml/library/x-hiperfparse/
5.http://effbot.org/zone/element-index.htm
http://effbot.org/zone/element-iterparse.htm
6. SAX : http://en.wikipedia.org/wiki/Simple_API_for_XML
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