Using Python Iterparse For Large XML Files
Solution 1
Try Liza Daly's fast_iter. After processing an element, elem
, it calls elem.clear()
to remove descendants and also removes preceding siblings.
def fast_iter(context, func, *args, **kwargs):
"""
http://lxml.de/parsing.html#modifying-the-tree
Based on Liza Daly's fast_iter
http://www.ibm.com/developerworks/xml/library/x-hiperfparse/
See also http://effbot.org/zone/element-iterparse.htm
"""
for event, elem in context:
func(elem, *args, **kwargs)
# It's safe to call clear() here because no descendants will be
# accessed
elem.clear()
# Also eliminate now-empty references from the root node to elem
for ancestor in elem.xpath('ancestor-or-self::*'):
while ancestor.getprevious() is not None:
del ancestor.getparent()[0]
del context
def process_element(elem):
print elem.xpath( 'description/text( )' )
context = etree.iterparse( MYFILE, tag='item' )
fast_iter(context,process_element)
Daly's article is an excellent read, especially if you are processing large XML files.
Edit: The fast_iter
posted above is a modified version of Daly's fast_iter
. After processing an element, it is more aggressive at removing other elements that are no longer needed.
The script below shows the difference in behavior. Note in particular that orig_fast_iter
does not delete the A1
element, while the mod_fast_iter
does delete it, thus saving more memory.
import lxml.etree as ET
import textwrap
import io
def setup_ABC():
content = textwrap.dedent('''\
<root>
<A1>
<B1></B1>
<C>1<D1></D1></C>
<E1></E1>
</A1>
<A2>
<B2></B2>
<C>2<D></D></C>
<E2></E2>
</A2>
</root>
''')
return content
def study_fast_iter():
def orig_fast_iter(context, func, *args, **kwargs):
for event, elem in context:
print('Processing {e}'.format(e=ET.tostring(elem)))
func(elem, *args, **kwargs)
print('Clearing {e}'.format(e=ET.tostring(elem)))
elem.clear()
while elem.getprevious() is not None:
print('Deleting {p}'.format(
p=(elem.getparent()[0]).tag))
del elem.getparent()[0]
del context
def mod_fast_iter(context, func, *args, **kwargs):
"""
http://www.ibm.com/developerworks/xml/library/x-hiperfparse/
Author: Liza Daly
See also http://effbot.org/zone/element-iterparse.htm
"""
for event, elem in context:
print('Processing {e}'.format(e=ET.tostring(elem)))
func(elem, *args, **kwargs)
# It's safe to call clear() here because no descendants will be
# accessed
print('Clearing {e}'.format(e=ET.tostring(elem)))
elem.clear()
# Also eliminate now-empty references from the root node to elem
for ancestor in elem.xpath('ancestor-or-self::*'):
print('Checking ancestor: {a}'.format(a=ancestor.tag))
while ancestor.getprevious() is not None:
print(
'Deleting {p}'.format(p=(ancestor.getparent()[0]).tag))
del ancestor.getparent()[0]
del context
content = setup_ABC()
context = ET.iterparse(io.BytesIO(content), events=('end', ), tag='C')
orig_fast_iter(context, lambda elem: None)
# Processing <C>1<D1/></C>
# Clearing <C>1<D1/></C>
# Deleting B1
# Processing <C>2<D/></C>
# Clearing <C>2<D/></C>
# Deleting B2
print('-' * 80)
"""
The improved fast_iter deletes A1. The original fast_iter does not.
"""
content = setup_ABC()
context = ET.iterparse(io.BytesIO(content), events=('end', ), tag='C')
mod_fast_iter(context, lambda elem: None)
# Processing <C>1<D1/></C>
# Clearing <C>1<D1/></C>
# Checking ancestor: root
# Checking ancestor: A1
# Checking ancestor: C
# Deleting B1
# Processing <C>2<D/></C>
# Clearing <C>2<D/></C>
# Checking ancestor: root
# Checking ancestor: A2
# Deleting A1
# Checking ancestor: C
# Deleting B2
study_fast_iter()
Solution 2
iterparse()
lets you do stuff while building the tree, that means that unless you remove what you don't need anymore, you'll still end up with the whole tree in the end.
For more information: read this by the author of the original ElementTree implementation (but it's also applicable to lxml)
Solution 3
Why won't you use the "callback" approach of sax?
Solution 4
In my experience, iterparse with or without element.clear
(see F. Lundh and L. Daly) cannot always cope with very large XML files: It goes well for some time, suddenly the memory consumption goes through the roof and a memory error occurs or the system crashes. If you encounter the same problem, maybe you can use the same solution: the expat parser. See also F. Lundh or the following example using OP’s XML snippet (plus two umlaute for checking that there are no encoding issues):
import xml.parsers.expat
from collections import deque
def iter_xml(inpath: str, outpath: str) -> None:
def handle_cdata_end():
nonlocal in_cdata
in_cdata = False
def handle_cdata_start():
nonlocal in_cdata
in_cdata = True
def handle_data(data: str):
nonlocal in_cdata
if not in_cdata and open_tags and open_tags[-1] == 'desc':
data = data.replace('\\', '\\\\').replace('\n', '\\n')
outfile.write(data + '\n')
def handle_endtag(tag: str):
while open_tags:
open_tag = open_tags.pop()
if open_tag == tag:
break
def handle_starttag(tag: str, attrs: 'Dict[str, str]'):
open_tags.append(tag)
open_tags = deque()
in_cdata = False
parser = xml.parsers.expat.ParserCreate()
parser.CharacterDataHandler = handle_data
parser.EndCdataSectionHandler = handle_cdata_end
parser.EndElementHandler = handle_endtag
parser.StartCdataSectionHandler = handle_cdata_start
parser.StartElementHandler = handle_starttag
with open(inpath, 'rb') as infile:
with open(outpath, 'w', encoding = 'utf-8') as outfile:
parser.ParseFile(infile)
iter_xml('input.xml', 'output.txt')
input.xml:
<root>
<item>
<title>Item 1</title>
<desc>Description 1ä</desc>
</item>
<item>
<title>Item 2</title>
<desc>Description 2ü</desc>
</item>
</root>
output.txt:
Description 1ä
Description 2ü
Admin
Updated on July 17, 2022Comments
-
Admin almost 2 years
I need to write a parser in Python that can process some extremely large files ( > 2 GB ) on a computer without much memory (only 2 GB). I wanted to use iterparse in lxml to do it.
My file is of the format:
<item> <title>Item 1</title> <desc>Description 1</desc> </item> <item> <title>Item 2</title> <desc>Description 2</desc> </item>
and so far my solution is:
from lxml import etree context = etree.iterparse( MYFILE, tag='item' ) for event, elem in context : print elem.xpath( 'description/text( )' ) del context
Unfortunately though, this solution is still eating up a lot of memory. I think the problem is that after dealing with each "ITEM" I need to do something to cleanup empty children. Can anyone offer some suggestions on what I might do after processing my data to properly cleanup?
-
bioslime over 9 yearsNeat. Yet, incase the element that we specify
tag='item'
does not exist and the XML is quite large there is a substantial memory build up that is not getting freed. I assume that the tree builds up and as no end event is trigged we get the whole XMl in memory. Is there any fix to that? -
unutbu over 9 years@bioslime: Not that I know of. Usually parsing XML requires that you know the format of the XML a priori.
-
unutbu over 9 years@bioslime: If you know some tag exists and wish to clear those to save memory, you could use
iterparse
to iterate over those tags, and then calliterwalk
inside the callback function to search foritem
tags. That way, you could search for the unknown tag while still saving some memory. But you would still have to know that some tag exists. Here is an example which uses this approach. -
bioslime over 9 years@unutbu: Okay, i'll have a look. I actually do know the format but in some XMLs all occourences of an element are
<item xsi:nil="true"/>
and not<item></item>
. For now i do a simple precheck: Open the file, iterate trough each line and check if<item>
is in it. If so break out of the loop. If not i'll later on skip thefor event, elem in context
. -
unutbu over 9 years@bioslime: Have you tried using
tag='item'
without the precheck?iterparse
will find those items either way, sofast_iter
will clear Elements asitem
s get processed. Handling all XMLs this way may be faster than doing prechecks, depending on the ratio of hits-to-duds. -
Zach Schulze over 6 yearsHow can a solution like this be used to handle child elements of an item? They appear to get cleared before we can use them.