I'm very new to python and I need to parse some dirty xml files which need sanitising first.
I have the following python code:
import arff
import xml.etree.ElementTree
import re
totstring=""
with open('input.sgm', 'r') as inF:
for line in inF:
string=re.sub("[^0-9a-zA-Z<>/\s=!-\"\"]+","", line)
totstring+=string
data=xml.etree.ElementTree.fromstring(totstring)
print data
file.close
which parses:
<!DOCTYPE lewis SYSTEM "lewis.dtd">
<REUTERS TOPICS="YES" LEWISSPLIT="TRAIN" CGISPLIT="TRAINING-SET" OLDID="5544" NEWID="1">
<DATE>26-FEB-1987 15:01:01.79</DATE>
<TOPICS><D>cocoa</D></TOPICS>
<PLACES><D>el-salvador</D><D>usa</D><D>uruguay</D></PLACES>
<PEOPLE></PEOPLE>
<ORGS></ORGS>
<EXCHANGES></EXCHANGES>
<COMPANIES></COMPANIES>
<UNKNOWN>
C T
f0704reute
u f BC-BAHIA-COCOA-REVIEW 02-26 0105</UNKNOWN>
<TEXT>
<TITLE>BAHIA COCOA REVIEW</TITLE>
<DATELINE> SALVADOR, Feb 26 - </DATELINE><BODY>Showers continued throughout the week in
the Bahia cocoa zone, alleviating the drought since early
January and improving prospects for the coming temporao,
although normal humidity levels have not been restored,
Comissaria Smith said in its weekly review.
The dry period means the temporao will be late this year.
Arrivals for the week ended February 22 were 155,221 bags
of 60 kilos making a cumulative total for the season of 5.93
mln against 5.81 at the same stage last year. Again it seems
that cocoa delivered earlier on consignment was included in the
arrivals figures.
Comissaria Smith said there is still some doubt as to how
much old crop cocoa is still available as harvesting has
practically come to an end. With total Bahia crop estimates
around 6.4 mln bags and sales standing at almost 6.2 mln there
are a few hundred thousand bags still in the hands of farmers,
middlemen, exporters and processors.
There are doubts as to how much of this cocoa would be fit
for export as shippers are now experiencing dificulties in
obtaining +Bahia superior+ certificates.
In view of the lower quality over recent weeks farmers have
sold a good part of their cocoa held on consignment.
Comissaria Smith said spot bean prices rose to 340 to 350
cruzados per arroba of 15 kilos.
Bean shippers were reluctant to offer nearby shipment and
only limited sales were booked for March shipment at 1,750 to
1,780 dlrs per tonne to ports to be named.
New crop sales were also light and all to open ports with
June/July going at 1,850 and 1,880 dlrs and at 35 and 45 dlrs
under New York july, Aug/Sept at 1,870, 1,875 and 1,880 dlrs
per tonne FOB.
Routine sales of butter were made. March/April sold at
4,340, 4,345 and 4,350 dlrs.
April/May butter went at 2.27 times New York May, June/July
at 4,400 and 4,415 dlrs, Aug/Sept at 4,351 to 4,450 dlrs and at
2.27 and 2.28 times New York Sept and Oct/Dec at 4,480 dlrs and
2.27 times New York Dec, Comissaria Smith said.
Destinations were the U.S., Covertible currency areas,
Uruguay and open ports.
Cake sales were registered at 785 to 995 dlrs for
March/April, 785 dlrs for May, 753 dlrs for Aug and 0.39 times
New York Dec for Oct/Dec.
Buyers were the U.S., Argentina, Uruguay and convertible
currency areas.
Liquor sales were limited with March/April selling at 2,325
and 2,380 dlrs, June/July at 2,375 dlrs and at 1.25 times New
York July, Aug/Sept at 2,400 dlrs and at 1.25 times New York
Sept and Oct/Dec at 1.25 times New York Dec, Comissaria Smith
said.
Total Bahia sales are currently estimated at 6.13 mln bags
against the 1986/87 crop and 1.06 mln bags against the 1987/88
crop.
Final figures for the period to February 28 are expected to
be published by the Brazilian Cocoa Trade Commission after
carnival which ends midday on February 27.
Reuter
</BODY></TEXT>
</REUTERS>
How can I now go about getting just the text from inside the body tag?
All the tutorials i have seen rely on reading the xml directly from a file so that Elementtree.parse works. As I am trying to parse from a string this will not work and this breaks a lot of tutorials I have read.
Thanks very much
If you don't care about the particular structure of a (potentially messy) XML document and just want to quickly get the contents of a given tag/element, you may want to try the BeautifulSoup module.
import BeautifulSoup
from BeautifulSoup import BeautifulSoup
soup = BeautifulSoup(totstring)
body = soup.find("body")
bodytext = body.text
Your first clue could be when you get messages like this...
>>> from xml.etree import ElementTree
>>> parse = ElementTree.parse('foo.xml')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.6/xml/etree/ElementTree.py", line 862, in parse
tree.parse(source, parser)
File "/usr/lib/python2.6/xml/etree/ElementTree.py", line 586, in parse
parser.feed(data)
File "/usr/lib/python2.6/xml/etree/ElementTree.py", line 1245, in feed
self._parser.Parse(data, 0)
xml.parsers.expat.ExpatError: reference to invalid character number: line 11, column 0
>>>
This error comes from invalid characters in the XML source. You need to clean up the invalid characters (see fix_xml.py at bottom of my answer).
After you have clean XML, it's pretty easy. You should use StringIO to treat strings as files:
>>> from xml.etree import ElementTree
>>> from StringIO import StringIO
>>> text = open('foo.xml', 'r').read()
>>> tree = ElementTree.parse(StringIO(text))
>>> tree.find('//BODY')
<Element BODY at b723cf2c>
>>> tree.find('//BODY').text
'Showers continued throughout the week in\nthe Bahia cocoa zone, alleviating the drought since early\nJanuary and improving prospects for the coming temporao,\nalthough normal humidity levels have not been restored,\nComissaria Smith said in its weekly review.\n The dry period means the temporao will be late this year.\n Arrivals for the week ended February 22 were 155,221 bags\nof 60 kilos making a cumulative total for the season of 5.93\nmln against 5.81 at the same stage last year. Again it seems\nthat cocoa delivered earlier on consignment was included in the\narrivals figures.\n Comissaria Smith said there is still some doubt as to how\nmuch old crop cocoa is still available as harvesting has\npractically come to an end. With total Bahia crop estimates\naround 6.4 mln bags and sales standing at almost 6.2 mln there\nare a few hundred thousand bags still in the hands of farmers,\nmiddlemen, exporters and processors.\n There are doubts as to how much of this cocoa would be fit\nfor export as shippers are now experiencing dificulties in\nobtaining +Bahia superior+ certificates.\n In view of the lower quality over recent weeks farmers have\nsold a good part of their cocoa held on consignment.\n Comissaria Smith said spot bean prices rose to 340 to 350\ncruzados per arroba of 15 kilos.\n Bean shippers were reluctant to offer nearby shipment and\nonly limited sales were booked for March shipment at 1,750 to\n1,780 dlrs per tonne to ports to be named.\n New crop sales were also light and all to open ports with\nJune/July going at 1,850 and 1,880 dlrs and at 35 and 45 dlrs\nunder New York july, Aug/Sept at 1,870, 1,875 and 1,880 dlrs\nper tonne FOB.\n Routine sales of butter were made. March/April sold at\n4,340, 4,345 and 4,350 dlrs.\n April/May butter went at 2.27 times New York May, June/July\nat 4,400 and 4,415 dlrs, Aug/Sept at 4,351 to 4,450 dlrs and at\n2.27 and 2.28 times New York Sept and Oct/Dec at 4,480 dlrs and\n2.27 times New York Dec, Comissaria Smith said.\n Destinations were the U.S., Covertible currency areas,\nUruguay and open ports.\n Cake sales were registered at 785 to 995 dlrs for\nMarch/April, 785 dlrs for May, 753 dlrs for Aug and 0.39 times\nNew York Dec for Oct/Dec.\n Buyers were the U.S., Argentina, Uruguay and convertible\ncurrency areas.\n Liquor sales were limited with March/April selling at 2,325\nand 2,380 dlrs, June/July at 2,375 dlrs and at 1.25 times New\nYork July, Aug/Sept at 2,400 dlrs and at 1.25 times New York\nSept and Oct/Dec at 1.25 times New York Dec, Comissaria Smith\nsaid.\n Total Bahia sales are currently estimated at 6.13 mln bags\nagainst the 1986/87 crop and 1.06 mln bags against the 1987/88\ncrop.\n Final figures for the period to February 28 are expected to\nbe published by the Brazilian Cocoa Trade Commission after\ncarnival which ends midday on February 27.\n Reuter\n'
>>>
I removed the following characters from the XML source to clean it up...
(py26_default)[mpenning@Bucksnort ~]$ python fix_xml.py foo.xml
bar.xml
343 
347 
351 
359 
364 
369 
378 
444 
3393 
(py26_default)[mpenning@Bucksnort ~]$
Keep in mind that there are other ways of doing this... lxml.soupparser also cleans up bad XML. Sample lxml.soupparser usage
from lxml.html import soupparser
from StringIO import StringIO
try:
parser = XMLParser(ns_clean=True, recover=True)
tree = ET.parse(StringIO(text), parser)
except UnicodeDecodeError:
tree = soupparser.parse(StringIO(text))
Cleaned up xml
<!DOCTYPE lewis SYSTEM "lewis.dtd">
<REUTERS TOPICS="YES" LEWISSPLIT="TRAIN" CGISPLIT="TRAINING-SET" OLDID="5544" NEWID="1">
<DATE>26-FEB-1987 15:01:01.79</DATE>
<TOPICS><D>cocoa</D></TOPICS>
<PLACES><D>el-salvador</D><D>usa</D><D>uruguay</D></PLACES>
<PEOPLE></PEOPLE>
<ORGS></ORGS>
<EXCHANGES></EXCHANGES>
<COMPANIES></COMPANIES>
<UNKNOWN>
C T
f0704reute
u f BC-BAHIA-COCOA-REVIEW 02-26 0105</UNKNOWN>
<TEXT>
<TITLE>BAHIA COCOA REVIEW</TITLE>
<DATELINE> SALVADOR, Feb 26 - </DATELINE><BODY>Showers continued throughout the week in
the Bahia cocoa zone, alleviating the drought since early
January and improving prospects for the coming temporao,
although normal humidity levels have not been restored,
Comissaria Smith said in its weekly review.
The dry period means the temporao will be late this year.
Arrivals for the week ended February 22 were 155,221 bags
of 60 kilos making a cumulative total for the season of 5.93
mln against 5.81 at the same stage last year. Again it seems
that cocoa delivered earlier on consignment was included in the
arrivals figures.
Comissaria Smith said there is still some doubt as to how
much old crop cocoa is still available as harvesting has
practically come to an end. With total Bahia crop estimates
around 6.4 mln bags and sales standing at almost 6.2 mln there
are a few hundred thousand bags still in the hands of farmers,
middlemen, exporters and processors.
There are doubts as to how much of this cocoa would be fit
for export as shippers are now experiencing dificulties in
obtaining +Bahia superior+ certificates.
In view of the lower quality over recent weeks farmers have
sold a good part of their cocoa held on consignment.
Comissaria Smith said spot bean prices rose to 340 to 350
cruzados per arroba of 15 kilos.
Bean shippers were reluctant to offer nearby shipment and
only limited sales were booked for March shipment at 1,750 to
1,780 dlrs per tonne to ports to be named.
New crop sales were also light and all to open ports with
June/July going at 1,850 and 1,880 dlrs and at 35 and 45 dlrs
under New York july, Aug/Sept at 1,870, 1,875 and 1,880 dlrs
per tonne FOB.
Routine sales of butter were made. March/April sold at
4,340, 4,345 and 4,350 dlrs.
April/May butter went at 2.27 times New York May, June/July
at 4,400 and 4,415 dlrs, Aug/Sept at 4,351 to 4,450 dlrs and at
2.27 and 2.28 times New York Sept and Oct/Dec at 4,480 dlrs and
2.27 times New York Dec, Comissaria Smith said.
Destinations were the U.S., Covertible currency areas,
Uruguay and open ports.
Cake sales were registered at 785 to 995 dlrs for
March/April, 785 dlrs for May, 753 dlrs for Aug and 0.39 times
New York Dec for Oct/Dec.
Buyers were the U.S., Argentina, Uruguay and convertible
currency areas.
Liquor sales were limited with March/April selling at 2,325
and 2,380 dlrs, June/July at 2,375 dlrs and at 1.25 times New
York July, Aug/Sept at 2,400 dlrs and at 1.25 times New York
Sept and Oct/Dec at 1.25 times New York Dec, Comissaria Smith
said.
Total Bahia sales are currently estimated at 6.13 mln bags
against the 1986/87 crop and 1.06 mln bags against the 1987/88
crop.
Final figures for the period to February 28 are expected to
be published by the Brazilian Cocoa Trade Commission after
carnival which ends midday on February 27.
Reuter
</BODY></TEXT>
</REUTERS>
John Machin's bad XML finder (fix_xml.py)
As John Machin mentions in this answer, some characters are not valid XML; this is a script he wrote to help find invalid XML characters.
# coding: ascii
# Find numeric character references that refer to Unicode code points
# that are not valid in XML.
# Get byte offsets for seeking etc in undecoded file bytestreams.
# Get unicode offsets for checking against ElementTree error message,
# **IF** your input file is small enough.
BYTE_OFFSETS = True
import sys, re, codecs
fname = sys.argv[1]
print fname
if BYTE_OFFSETS:
text = open(fname, "rb").read()
else:
# Assumes file is encoded in UTF-8.
text = codecs.open(fname, "rb", "utf8").read()
rx = re.compile("&#([0-9]+);|&#x([0-9a-fA-F]+);")
endpos = len(text)
pos = 0
while pos < endpos:
m = rx.search(text, pos)
if not m: break
mstart, mend = m.span()
target = m.group(1)
if target:
num = int(target)
else:
num = int(m.group(2), 16)
# #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] | [#x10000-#x10FFFF]
if not(num in (0x9, 0xA, 0xD) or 0x20 <= num <= 0xD7FF
or 0xE000 <= num <= 0xFFFD or 0x10000 <= num <= 0x10FFFF):
print mstart, m.group()
pos = mend
I don't know if this will still help you, but I was running into a similar problem and needed to get my xml data into an element tree, not BeautifulSoup or lxml's soupparser. I didn't want to have to make two passes through my xml file either. So, I found out how to build a custom XMLParser for ElementTree (not cElementTree, though). Using some of Mike's code I created an XMLParser class that can intercept the character data and filter out invalid characters before going through the parser.
Here you go:
import xml.etree.ElementTree as ET
import sys
import re
class MyXMLParser(ET.XMLParser):
rx = re.compile("&#([0-9]+);|&#x([0-9a-fA-F]+);")
def feed(self,data):
m = self.rx.search(data)
if m is not None:
target = m.group(1)
if target:
num = int(target)
else:
num = int(m.group(2), 16)
if not(num in (0x9, 0xA, 0xD) or 0x20 <= num <= 0xD7FF
or 0xE000 <= num <= 0xFFFD or 0x10000 <= num <= 0x10FFFF):
# is invalid xml character, cut it out of the stream
print 'removing %s' % m.group()
mstart, mend = m.span()
mydata = data[:mstart] + data[mend:]
else:
mydata = data
super(MyXMLParser,self).feed(mydata)
parser = MyXMLParser(encoding='utf-8')
xml_filename = sys.argv[1]
xml_etree = ET.parse(xml_filename, parser=parser)
