I have a script which is suppose to extract some terms from XML files from a list of URLs.
All the URL's give access to XML data.
It is working fine at first opening, parsing and extracting correctly but then get interrupted in the process by some XML files with this error:
File "<stdin>", line 18, in <module>
File "lxml.etree.pyx", line 2953, in lxml.etree.parse (src/lxml/lxml.etree.c:56204)
File "parser.pxi", line 1555, in lxml.etree._parseDocument (src/lxml/lxml.etree.c:82511)
File "parser.pxi", line 1585, in lxml.etree._parseFilelikeDocument (src/lxml/lxml.etree.c:82832)
File "parser.pxi", line 1468, in lxml.etree._parseDocFromFilelike (src/lxml/lxml.etree.c:81688)
File "parser.pxi", line 1024, in lxml.etree._BaseParser._parseDocFromFilelike (src/lxml/lxml.etree.c:78735)
File "parser.pxi", line 569, in lxml.etree._ParserContext._handleParseResultDoc (src/lxml/lxml.etree.c:74472)
File "parser.pxi", line 650, in lxml.etree._handleParseResult (src/lxml/lxml.etree.c:75363)
File "parser.pxi", line 590, in lxml.etree._raiseParseError (src/lxml/lxml.etree.c:74696)
lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1
From my search it might be because some XML files have white spaces but i'm not sure if it is the problem. I can't tell which files give the error.
Is there a way to get around this error?
Here is my script:
URLlist = ["http://www.uniprot.org/uniprot/"+x+".xml" for x in IDlist]
for id, item in zip(IDlist, URLlist):
goterm_location = []
goterm_function = []
goterm_process = []
location_list[id] = []
function_list[id] = []
biological_list[id] = []
try:
textfile = urllib2.urlopen(item);
except urllib2.HTTPError:
print("URL", item, "could not be read.")
continue
#Try to solve empty line error#
tree = etree.parse(textfile);
#root = tree.getroot()
for node in tree.iter('{http://uniprot.org/uniprot}dbReference'):
if node.attrib.get('type') == 'GO':
for child in node:
value = child.attrib.get('value');
if value.startswith('C:'):
goterm_C = node.attrib.get('id')
if goterm_C:
location_list[id].append(goterm_C);
if value.startswith('F:'):
goterm_F = node.attrib.get('id')
if goterm_F:
function_list[id].append(goterm_F);
if value.startswith('P:'):
goterm_P = node.attrib.get('id')
if goterm_P:
biological_list[id].append(goterm_P);
I have tried:
tree = etree.iterparse(textfile, events = ("start","end"));
OR
parser = etree.XMLParser(remove_blank_text=True)
tree = etree.parse(textfile, parser)
Without success.
Any help would be greatly appreciated
I can't tell which files give the error
Debug by printing the name of the file/URL prior to parsing. Then you'll see which file(s) cause the error.
Also, read the error message:
lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1
this suggests that the downloaded XML file is empty. Once you have determined the URL(s) that cause the problem, try downloading the file and check its contents. I suspect it might be empty.
You can ignore problematic files (empty or otherwise syntactically invalid) by using a try/except block when parsing:
try:
tree = etree.parse(textfile)
except lxml.etree.XMLSyntaxError:
print 'Skipping invalid XML from URL {}'.format(item)
continue # go on to the next URL
Or you could check just for empty files by checking the 'Content-length' header, or even by reading the resource returned by urlopen(), but I think that the above is better as it will also catch other potential errors.
I got the same error message in Python 3.6
lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1
In my case the xml file is not empty. Issue is because of encoding,
Initially used utf-8,
from lxml import etree
etree.iterparse(my_xml_file.xml, tag='MyTag', encoding='utf-8')
changing encoding to iso-8859-1 solved my issue,
etree.iterparse(my_xml_file.xml, tag='MyTag', encoding='iso-8859-1')
Related
I'm literally new to Python and I have encounter something that I am not sure how to resolve I'm sure it must be a simple fix but haven't found an solution and hope someone with more knowledge in Python will be able to help.
My request:
...
contacts = requests.post(url,data=readContactsXml,headers=headers);
#print (contacts.content) ;
outF = open("contact.xml", "wb")
outF.write(contacts.content)
outF.close();
all is fine until with the above until I have to manipulate the data before saving it :
E.G:
...
contacts = requests.post(url,data=readContactsXml,headers=headers);
import xml.etree.ElementTree as ET
# contacts.encoding = 'utf-8'
parser = ET.XMLParser(encoding="UTF-8")
tree = ET.fromstring(contacts.content, parser=parser)
root = tree.getroot()
for item in root[0][0].findall('.//fields'):
if item[0].text == 'maching-text-here':
if not item[1].text:
item[1].text = 'N/A'
print(item[1].text)
#print (contacts.content) ;
outF = open("contact.xml", "wb")
outF.write(contacts.content)
outF.close();
in the above I literally replacing empty value with value 'N/A'
the error that I'm receiving is:
Traceback (most recent call last):
File "Desktop/PythonTests/test.py", line 107, in <module>
tree = ET.fromstring(contacts.content, parser=parser)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xml/etree/ElementTree.py", line 1311, in XML
parser.feed(text)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xml/etree/ElementTree.py", line 1659, in feed
self._raiseerror(v)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xml/etree/ElementTree.py", line 1523, in _raiseerror
raise err
xml.etree.ElementTree.ParseError: not well-formed (invalid token): line 1, column 192300
looking around this column I can see a text with characters E.G: Sinéd, É is a problem here and actually when I just save this xml file and open in the browser I get kind of same error round about give or take the same column missing by 2:
This page contains the following errors:
error on line 1 at column 192298: Encoding error
Below is a rendering of the page up to the first error.
I wonder What I can do with data xml response that contain data with characters ?
Anyone any help Appreciated!
Found my answer after digging stack overflow:
I've modified:
FROM:
tree = ET.fromstring(contacts.content, parser=parser)
TO:
tree = ElementTree(fromstring(contacts.content))
REF:https://stackoverflow.com/questions/33962620/elementtree-returns-element-instead-of-elementtree/44483259#44483259
Hi I'm trying to parse all XML files in a given directory using python. I am able to parse one file at a time but that would be 'impossible' for me to do due to the large number of files i.e. it works when I pre-define the tree and root, however not when I try to run for all the code.
This is what I implemented so far:
import xml.etree.ElementTree as ET
import os
directory = "C:/Users/danie/Desktop/NLP/blogs/"
def clean_dir(directory):
path = os.listdir(directory)
print(path)
for filename in path:
tree = ET.parse(filename)
root = tree.getroot()
doc_parser(root)
post_list = []
def doc_parser(root):
for child in root.findall('post'):
post_list.append(child.text)
clean_dir(directory)
print(post_list[0])
The error I'm getting as follows:
File "D:\Anaconda\envs\Deep Learning New\lib\site-packages\IPython\core\interactiveshell.py", line 3326, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-91-fce6b0119ea7>", line 1, in <module>
runfile('C:/Users/danie/Desktop/NLP/blogs/Parser_Tes.py', wdir='C:/Users/danie/Desktop/NLP/blogs')
File "D:\Anaconda\envs\Deep Learning New\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 827, in runfile
execfile(filename, namespace)
File "D:\Anaconda\envs\Deep Learning New\lib\site-packages\spyder_kernels\customize\spydercustomize.py", line 110, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/danie/Desktop/NLP/blogs/Parser_Tes.py", line 19, in <module>
clean_dir(directory)
File "C:/Users/danie/Desktop/NLP/blogs/Parser_Tes.py", line 9, in clean_dir
tree = ET.parse(filename)
File "D:\Anaconda\envs\Deep Learning New\lib\xml\etree\ElementTree.py", line 1196, in parse
tree.parse(source, parser)
File "D:\Anaconda\envs\Deep Learning New\lib\xml\etree\ElementTree.py", line 597, in parse
self._root = parser._parse_whole(source)
File "<string>", line unknown
ParseError: not well-formed (invalid token): line 103, column 225
In terms of printing out the path, all correct filenames are being printed out. Some of which are:
['1000331.female.37.indUnk.Leo.xml', '1000866.female.17.Student.Libra.xml', '1004904.male.23.Arts.Capricorn.xml', '1005076.female.25.Arts.Cancer.xml', '1005545.male.25.Engineering.Sagittarius.xml', '1007188.male.48.Religion.Libra.xml', '100812.female.26.Architecture.Aries.xml', '1008329.female.16.Student.Pisces.xml', '1009572.male.25.indUnk.Cancer.xml', '1011153.female.27.Technology.Virgo.xml', '1011289.female.25.indUnk.Libra.xml', '1011311.female.17.indUnk.Scorpio.xml', '1013637.male.17.RealEstate.Virgo.xml', '1015252.female.23.indUnk.Pisces.xml', '1015556.male.34.Technology.Virgo.xml', '1016560.male.41.Publishing.Sagittarius.xml', '1016738.male.26.Publishing.Libra.xml', '1016787.female.24.Communications-Media.Leo.xml', '1019224.female.27.RealEstate.Libra.xml', '1019622.female.24.indUnk.Aquarius.xml', '1019710.male.16.Student.Pisces.xml', '1021779.female.25.indUnk.Scorpio.xml', '1022037.male.23.indUnk.Cancer.xml', '1022086.female.17.Student.Cancer.xml', '1024234.female.17.indUnk.Libra.xml', '1025783.female.17.Student.Gemini.xml', '1026164.female.23.Education.Aries.xml', '1026443.female.15.Student.Scorpio.xml', '1028027.female.16.indUnk.Libra.xml', '1028257.male.26.Education.Aries.xml', '1029959.male.17.indUnk.Aries.xml', '1031806.male.17.Technology.Sagittarius.xml', '1032153.male.27.Technology.Pisces.xml', '1032591.female.24.Banking.Aquarius.xml', '1032824.female.15.Student.Libra.xml', '1034874.female.43.Publishing.Capricorn.xml', '1039136.male.24.Student.Capricorn.xml', '1039908.female.16.indUnk.Gemini.xml', '1040084.male.17.indUnk.Taurus.xml', '1042993.male.15.Student.Sagittarius.xml', '1043329.male.23.Government.Pisces.xml', '1043569.male.26.indUnk.Virgo.xml', '1043785.female.26.Biotech.Leo.xml', '1044338.female.23.Student.Leo.xml', '1045289.female.25.Arts.Aquarius.xml', '1045316.male.27.Non-Profit.Capricorn.xml', '1045831.male.23.Student.Libra.xml', '1046946.female.25.Arts.Virgo.xml', '1047241.male.16.indUnk.Aries.xml', '1050060.female.24.Student.Pisces.xml', '1051122.female.17.Student.Libra.xml', '1052611.male.23.Student.Aries.xml', '1054833.female.24.indUnk.Scorpio.xml', '1055228.female.16.Student.Cancer.xml', '1056232.female.17.indUnk.Aquarius.xml', '1056581.female.26.indUnk.Leo.xml', ....]
So I took the advice of both #wundermahn and #Kevin and use try...except. This is the output now. i.e. 482 from 19320 items. The issue now, when I try to print out a certain element from the list post_list[]. I'm getting the following error:
IndexError: list index out of range
Files with errors:
ERROR ON FILE: 669116.female.26.indUnk.Gemini.xml
ERROR ON FILE: 669514.female.27.indUnk.Sagittarius.xml
ERROR ON FILE: 669656.female.23.Advertising.Aries.xml
ERROR ON FILE: 669719.male.26.Science.Taurus.xml
ERROR ON FILE: 669764.female.17.indUnk.Sagittarius.xml
ERROR ON FILE: 670277.female.27.Education.Sagittarius.xml
ERROR ON FILE: 670314.male.24.indUnk.Leo.xml
ERROR ON FILE: 670684.male.24.Student.Libra.xml
ERROR ON FILE: 671748.male.27.Communications-Media.Aries.xml
ERROR ON FILE: 673093.male.27.Construction.Scorpio.xml
ERROR ON FILE: 673235.male.37.Internet.Capricorn.xml
ERROR ON FILE: 67459.male.34.Arts.Capricorn.xml
ERROR ON FILE: 674684.female.23.Religion.Libra.xml
Further checked and printed out post_list, for some reason the data is not being appended and it is empty.
Thanks again!
#Kevin was correct in his comment that this error relates to the ElementTree object not being able to parse the document correctly. Something is not "true XML", and it could be something as simple as just an odd, non-unicode character or something.
What you can try to do to help debug is:
import xml.etree.ElementTree as ET
import os
directory = "C:/Users/danie/Desktop/NLP/blogs/"
def clean_dir(directory):
path = os.listdir(directory)
print(path)
for filename in path:
try:
tree = ET.parse(filename)
root = tree.getroot()
doc_parser(root)
except:
print("ERROR ON FILE: {}".format(filename))
post_list = []
def doc_parser(root):
for child in root.findall('post'):
post_list.append(child.text)
clean_dir(directory)
print(post_list[0])
Adding in a try...except statement will try each of the files, and if there is an error, print out which file is causing the error.
I don't have any data to test, but this should fix the error.
I'm trying to parse XML returned by the Stanford CoreNLP in python using the xml.etree.ElementTree module, but I seem to keep running into this error.
Here is the error I get:
File "my_script.py", line 5
root = ET.fromstring(content)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xml/etree/ElementTree.py", line 1300, in XML
parser.feed(text)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xml/etree/ElementTree.py", line 1642, in feed
self._raiseerror(v)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror
raise err
xml.etree.ElementTree.ParseError: not well-formed (invalid token): line 4473, column 19
I checked out out what's on line 4473 in the XML file:
<word>5 1/2</word>
Column 19 starts at the 5.
I assume the problem is due to the forward slash in the number 5 1/2 since this is the first instance the 5 1/2 occurs in the XML file. Does anyone know a way I can still parse the XML file with the forward-slashes?
Here is the code also:
import xml.etree.ElementTree as ET
f = open("samplefiles/samplefile999.txt.xml","r");
content = f.read()
f.close();
root = ET.fromstring(content)
I'm trying to validate an XML file against an external DTD referenced in the doctype tag. Specifically:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE en-export SYSTEM "http://xml.evernote.com/pub/evernote-export3.dtd">
...the rest of the document...
I'm using Python 3.3 and the lxml module. From reading http://lxml.de/validation.html#validation-at-parse-time, I've thrown this together:
enexFile = open(sys.argv[2], mode="rb") # sys.argv[2] is the path to an XML file in local storage.
enexParser = etree.XMLParser(dtd_validation=True)
enexTree = etree.parse(enexFile, enexParser)
From what I understand of validation.html, the lxml library should now take care of retrieving the DTD and performing validation. But instead, I get this:
$ ./mapwrangler.py validate notes.enex
Traceback (most recent call last):
File "./mapwrangler.py", line 27, in <module>
enexTree = etree.parse(enexFile, enexParser)
File "lxml.etree.pyx", line 3239, in lxml.etree.parse (src/lxml/lxml.etree.c:69955)
File "parser.pxi", line 1769, in lxml.etree._parseDocument (src/lxml/lxml.etree.c:102257)
File "parser.pxi", line 1789, in lxml.etree._parseFilelikeDocument (src/lxml/lxml.etree.c:102516)
File "parser.pxi", line 1684, in lxml.etree._parseDocFromFilelike (src/lxml/lxml.etree.c:101442)
File "parser.pxi", line 1134, in lxml.etree._BaseParser._parseDocFromFilelike (src/lxml/lxml.etree.c:97069)
File "parser.pxi", line 582, in lxml.etree._ParserContext._handleParseResultDoc (src/lxml/lxml.etree.c:91275)
File "parser.pxi", line 683, in lxml.etree._handleParseResult (src/lxml/lxml.etree.c:92461)
File "parser.pxi", line 622, in lxml.etree._raiseParseError (src/lxml/lxml.etree.c:91757)
lxml.etree.XMLSyntaxError: Validation failed: no DTD found !, line 3, column 43
This surprises me, because if I turn off validation, then the document parses in just fine and I can do print(enexTree.docinfo.doctype) to get
$ ./mapwrangler.py validate notes.enex
<!DOCTYPE en-export SYSTEM "http://xml.evernote.com/pub/evernote-export3.dtd">
So it looks to me like there shouldn't be any problem finding the DTD.
Thanks for your help.
You need to add no_network=False when constructing the parser object. This option is set to True by default.
From the documentation of parser options at http://lxml.de/parsing.html#parsers:
no_network - prevent network access when looking up external documents (on by default)
For a reason I still don't know, my problem was related to where the XML catalog was located on my local file system.
In my case, I use an XML editor that has a tight integration with a component content management system (CCMS, in this case SDL Trisoft 2011 R2). When the editor connects to the CCMS, DTDs, catalog files and a bunch of other files are synced. These files end up on the local file system in:
C:\Users\[username]\AppData\Local\Trisoft\InfoShare Client\[id]\Config\DocTypes\catalog.xml
I could not get that to work. Simply COPYING the whole catalog to another location fixed things, and this works:
f = r"path/to/my/file.xml"
# set XML catatog file path
os.environ['XML_CATALOG_FILES'] = r'C:\DATA\Mydoctypes\catalog.xml'
# configure parser
parser = etree.XMLParser(dtd_validation=True, no_network=True)
# validate
try:
valid = etree.parse(f, parser=parser)
print("This file is valid against the DTD.")
except etree.XMLSyntaxError, error:
print("This file is INVALID against the DTD!")
print(error)
Obviously this is not ideal, but it works.
Could it be something to do with file permissions, or perhaps that good old "file path too long" problem in Windows? I have not tried whether a symbolic link would work.
I am using Windows 7, Python 2.7.11 and the version of lxml is (3.6.0).
I want to parse downloaded RSS with lxml, but I don't know how to handle with UnicodeDecodeError?
request = urllib2.Request('http://wiadomosci.onet.pl/kraj/rss.xml')
response = urllib2.urlopen(request)
response = response.read()
encd = chardet.detect(response)['encoding']
parser = etree.XMLParser(ns_clean=True,recover=True,encoding=encd)
tree = etree.parse(response, parser)
But I get an error:
tree = etree.parse(response, parser)
File "lxml.etree.pyx", line 2692, in lxml.etree.parse (src/lxml/lxml.etree.c:49594)
File "parser.pxi", line 1500, in lxml.etree._parseDocument (src/lxml/lxml.etree.c:71364)
File "parser.pxi", line 1529, in lxml.etree._parseDocumentFromURL (src/lxml/lxml.etree.c:71647)
File "parser.pxi", line 1429, in lxml.etree._parseDocFromFile (src/lxml/lxml.etree.c:70742)
File "parser.pxi", line 975, in lxml.etree._BaseParser._parseDocFromFile (src/lxml/lxml.etree.c:67
740)
File "parser.pxi", line 539, in lxml.etree._ParserContext._handleParseResultDoc (src/lxml/lxml.etr
ee.c:63824)
File "parser.pxi", line 625, in lxml.etree._handleParseResult (src/lxml/lxml.etree.c:64745)
File "parser.pxi", line 559, in lxml.etree._raiseParseError (src/lxml/lxml.etree.c:64027)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc5 in position 97: ordinal not in range(128)
I ran into a similar problem, and it turns out this has NOTHING to do with encodings. What's happening is this - lxml is throwing you a totally unrelated error. In this case, the error is that the .parse function expects a filename or URL, and not a string with the contents itself. However, when it tries to print out the error, it chokes on non-ascii characters and shows that completely confusing error message. It is highly unfortunate and other people have commented on this issue here:
https://mailman-mail5.webfaction.com/pipermail/lxml/2009-February/004393.html
Luckily, yours is a very easy fix. Just replace .parse with .fromstring and you should be totally good to go:
request = urllib2.Request('http://wiadomosci.onet.pl/kraj/rss.xml')
response = urllib2.urlopen(request)
response = response.read()
encd = chardet.detect(response)['encoding']
parser = etree.XMLParser(ns_clean=True,recover=True,encoding=encd)
## lxml Y U NO MAKE SENSE!!!
tree = etree.fromstring(response, parser)
Just tested this on my machine and it worked fine. Hope it helps!
It's often easier to get the string loaded and sorted out for the lxml library first, and then call fromstring on it, rather than rely on the lxml.etree.parse() function and its difficult to manage encoding options.
This particular rss file begins with the encoding declaration, so everything should just work:
<?xml version="1.0" encoding="utf-8"?>
The following code shows some of the different variations you can apply to make etree parse for different encodings. You can also request it to write out different encodings too, which will appear in the headers.
import lxml.etree
import urllib2
request = urllib2.Request('http://wiadomosci.onet.pl/kraj/rss.xml')
response = urllib2.urlopen(request).read()
print [response]
# ['<?xml version="1.0" encoding="utf-8"?>\n<feed xmlns=... <title>Wiadomo\xc5\x9bci...']
uresponse = response.decode("utf8")
print [uresponse]
# [u'<?xml version="1.0" encoding="utf-8"?>\n<feed xmlns=... <title>Wiadomo\u015bci...']
tree = lxml.etree.fromstring(response)
res = lxml.etree.tostring(tree)
print [res]
# ['<feed xmlns="http://www.w3.org/2005/Atom">\n<title>Wiadomości...']
lres = lxml.etree.tostring(tree, encoding="latin1")
print [lres]
# ["<?xml version='1.0' encoding='latin1'?>\n<feed xmlns=...<title>Wiadomości...']
# works because the 38 character encoding declaration is sliced off
print lxml.etree.fromstring(uresponse[38:])
# throws ValueError(u'Unicode strings with encoding declaration are not supported.',)
print lxml.etree.fromstring(uresponse)
Code can be tried here:
http://scraperwiki.com/scrapers/lxml_and_encoding_declarations/edit/#
You should probably only be trying to define the character encoding as a last resort, since it's clear what the encoding is based on the XML prolog (if not by the HTTP headers.) Anyway, it's unnecessary to pass the encoding to etree.XMLParser unless you want to override the encoding; so get rid of the encoding parameter and it should work.
Edit: okay, the problem actually seems to be with lxml. The following works, for whatever reason:
parser = etree.XMLParser(ns_clean=True, recover=True)
etree.parse('http://wiadomosci.onet.pl/kraj/rss.xml', parser)