Re: [CODE4LIB] XML Parsing and Python
I ended up doing a regular expression find and replace function to replace all illegal xml characters with a dash or something. I was more disappointed in the fact that on the xml creation end, minidom was able to create non-compliant xml files. I assumed that if minidom could make it, it would be compliant but that doesn't seem to be the case. Now I have to add a find and replace function on the creation side to avoid this issue in the future. Good learning experience I guess. Thanks for all your suggestions. Mike Beccaria Systems Librarian Head of Digital Initiative Paul Smith's College 518.327.6376 mbecca...@paulsmiths.edu Become a friend of Paul Smith's Library on Facebook today! -Original Message- From: Code for Libraries [mailto:CODE4LIB@LISTSERV.ND.EDU] On Behalf Of Chris Beer Sent: Tuesday, March 05, 2013 1:48 PM To: CODE4LIB@LISTSERV.ND.EDU Subject: Re: [CODE4LIB] XML Parsing and Python I'll note that 0x is a UTF-8 non-character, and these noncharacters should never be included in text interchange between implementations. [1] I assume the OCR engine maybe using 0x when it can't recognize a character? So, it's not wrong for a parser to complain (or, not complain) about 0x, and you can just scrub the string like Jon suggests. Chris [1] http://en.wikipedia.org/wiki/Mapping_of_Unicode_characters#Noncharacters On 5 Mar, 2013, at 9:16 , Jon Stroop jstr...@princeton.edu wrote: Mike, I haven't used minidom extensively but my guess is that doc.toprettyxml(indent= ,encoding=utf-8) isn't actually changing the encoding because it can't parse the string in your content variable. I'm surprised that you're not getting tossed a UnicodeError, but The docs for Node.toxml() [1] might shed some light: To avoid UnicodeError exceptions in case of unrepresentable text data, the encoding argument should be specified as utf-8. So what happens if you're not explicit about the encoding, i.e. just doc.toprettyxml()? This would hopefully at least move your exception to a more appropriate place. In any case, one solution would be to scrub the string in your content variable to get rid of the invalid characters (hopefully they're insignificant). Maybe something like this: def unicode_filter(char): try: unicode(char, encoding='utf-8', errors='strict') return char except UnicodeDecodeError: return '' content = 'abc\xFF' content = ''.join(map(unicode_filter, content)) print content Not really my area of expertise, but maybe worth a shot -Jon 1. http://docs.python.org/2/library/xml.dom.minidom.html#xml.dom.minidom. Node.toxml -- Jon Stroop Digital Initiatives Programmer/Analyst Princeton University Library jstr...@princeton.edu On 03/04/2013 03:00 PM, Michael Beccaria wrote: I'm working on a project that takes the ocr data found in a pdf and places it in a custom xml file. I use Python scripts to create the xml file. Something like this (trimmed down a bit): from xml.dom.minidom import Document doc = Document() Page = doc.createElement(Page) doc.appendChild(Page) f = StringIO(txt) lines = f.readlines() for line in lines: word = doc.createElement(String) ... word.setAttribute(CONTENT,content) Page.appendChild(word) return doc.toprettyxml(indent= ,encoding=utf-8) This creates a file, simply, that looks like this: ?xml version=1.0 encoding=utf-8? Page HEIGHT=3296 WIDTH=2609 String CONTENT=BuffaloLaunch / String CONTENT=Club / String CONTENT=Offices / String CONTENT=Installed / ... /Page I am able to get this document to be created ok and saved to an xml file. The problem occurs when I try and have it read using the lxml library: from lxml import etree doc = etree.parse(filename) I am running across errors like XMLSyntaxError: Char 0x out of allowed range, line 94, column 19. Which when I look at the file, is true. There is a 0X character in the content field. How is a file able to be created using minidom (which I assume would create a valid xml file) and then failing when parsing with lxml? What should I do to fix this on the encoding side so that errors don't show up on the parsing side? Thanks, Mike How is the Mike Beccaria Systems Librarian Head of Digital Initiative Paul Smith's College 518.327.6376 mbecca...@paulsmiths.edu Become a friend of Paul Smith's Library on Facebook today!
Re: [CODE4LIB] XML Parsing and Python
On Thu, Mar 7, 2013 at 10:49 AM, Michael Beccaria
mbecca...@paulsmiths.eduwrote:
I ended up doing a regular expression find and replace function to replace
all illegal xml characters with a dash or something.
:(
A string translation map might be a better approach. Here's what I do as
one part of a general purpose text cleanup method.
{{{
illegal_unichrs = [ (0x00, 0x08), (0x0B, 0x1F), (0x7F, 0x84), (0x86, 0x9F),
(0xD800, 0xDFFF), (0xFDD0, 0xFDDF), (0xFFFE, 0x),
(0x1FFFE, 0x1), (0x2FFFE, 0x2), (0x3FFFE, 0x3),
(0x4FFFE, 0x4), (0x5FFFE, 0x5), (0x6FFFE, 0x6),
(0x7FFFE, 0x7), (0x8FFFE, 0x8), (0x9FFFE, 0x9),
(0xAFFFE, 0xA), (0xBFFFE, 0xB), (0xCFFFE, 0xC),
(0xDFFFE, 0xD), (0xEFFFE, 0xE), (0xE, 0xF),
(0x10FFFE, 0x10) ]
tmap = dict.fromkeys(r for start, end in illegal_unichrs for r in
range(start, end+1))
...
text = text.translate(tmap)
}}}
See the str.translate() method at
http://docs.python.org/2/library/stdtypes.html#string-methods
--jay
Re: [CODE4LIB] XML Parsing and Python
Hello Mike, I realize minidom is a pure python library, but I wonder if elementtree isn't preferred here since you're already using lxml? I think the latter must be based on the former. Or for a bit of a snark, try, e.g. http://blog.ianbicking.org/2008/03/30/python-html-parser-performance/ .. Bicking: I don't recommend using minidom for anything. -- Al Matthews Software Developer, Digital Services Unit Atlanta University Center, Robert W. Woodruff Library email: amatth...@auctr.edu; office: 1 404 978 2057 On 3/7/13 10:49 AM, Michael Beccaria mbecca...@paulsmiths.edu wrote: I ended up doing a regular expression find and replace function to replace all illegal xml characters with a dash or something. I was more disappointed in the fact that on the xml creation end, minidom was able to create non-compliant xml files. I assumed that if minidom could make it, it would be compliant but that doesn't seem to be the case. Now I have to add a find and replace function on the creation side to avoid this issue in the future. Good learning experience I guess. Thanks for all your suggestions. Mike Beccaria Systems Librarian Head of Digital Initiative Paul Smith's College 518.327.6376 mbecca...@paulsmiths.edu Become a friend of Paul Smith's Library on Facebook today! -Original Message- From: Code for Libraries [mailto:CODE4LIB@LISTSERV.ND.EDU] On Behalf Of Chris Beer Sent: Tuesday, March 05, 2013 1:48 PM To: CODE4LIB@LISTSERV.ND.EDU Subject: Re: [CODE4LIB] XML Parsing and Python I'll note that 0x is a UTF-8 non-character, and these noncharacters should never be included in text interchange between implementations. [1] I assume the OCR engine maybe using 0x when it can't recognize a character? So, it's not wrong for a parser to complain (or, not complain) about 0x, and you can just scrub the string like Jon suggests. Chris [1] http://en.wikipedia.org/wiki/Mapping_of_Unicode_characters#Noncharacters On 5 Mar, 2013, at 9:16 , Jon Stroop jstr...@princeton.edu wrote: Mike, I haven't used minidom extensively but my guess is that doc.toprettyxml(indent= ,encoding=utf-8) isn't actually changing the encoding because it can't parse the string in your content variable. I'm surprised that you're not getting tossed a UnicodeError, but The docs for Node.toxml() [1] might shed some light: To avoid UnicodeError exceptions in case of unrepresentable text data, the encoding argument should be specified as utf-8. So what happens if you're not explicit about the encoding, i.e. just doc.toprettyxml()? This would hopefully at least move your exception to a more appropriate place. In any case, one solution would be to scrub the string in your content variable to get rid of the invalid characters (hopefully they're insignificant). Maybe something like this: def unicode_filter(char): try: unicode(char, encoding='utf-8', errors='strict') return char except UnicodeDecodeError: return '' content = 'abc\xFF' content = ''.join(map(unicode_filter, content)) print content Not really my area of expertise, but maybe worth a shot -Jon 1. http://docs.python.org/2/library/xml.dom.minidom.html#xml.dom.minidom. Node.toxml -- Jon Stroop Digital Initiatives Programmer/Analyst Princeton University Library jstr...@princeton.edu On 03/04/2013 03:00 PM, Michael Beccaria wrote: I'm working on a project that takes the ocr data found in a pdf and places it in a custom xml file. I use Python scripts to create the xml file. Something like this (trimmed down a bit): from xml.dom.minidom import Document doc = Document() Page = doc.createElement(Page) doc.appendChild(Page) f = StringIO(txt) lines = f.readlines() for line in lines: word = doc.createElement(String) ... word.setAttribute(CONTENT,content) Page.appendChild(word) return doc.toprettyxml(indent= ,encoding=utf-8) This creates a file, simply, that looks like this: ?xml version=1.0 encoding=utf-8? Page HEIGHT=3296 WIDTH=2609 String CONTENT=BuffaloLaunch / String CONTENT=Club / String CONTENT=Offices / String CONTENT=Installed / ... /Page I am able to get this document to be created ok and saved to an xml file. The problem occurs when I try and have it read using the lxml library: from lxml import etree doc = etree.parse(filename) I am running across errors like XMLSyntaxError: Char 0x out of allowed range, line 94, column 19. Which when I look at the file, is true. There is a 0X character in the content field. How is a file able to be created using minidom (which I assume would create a valid xml file) and then failing when parsing with lxml? What should I do to fix this on the encoding side so that errors don't show up on the parsing side? Thanks, Mike How is the Mike Beccaria Systems Librarian Head of Digital Initiative Paul Smith's College 518.327.6376 mbecca
Re: [CODE4LIB] XML Parsing and Python
Mike, I haven't used minidom extensively but my guess is that doc.toprettyxml(indent= ,encoding=utf-8) isn't actually changing the encoding because it can't parse the string in your content variable. I'm surprised that you're not getting tossed a UnicodeError, but The docs for Node.toxml() [1] might shed some light: To avoid UnicodeError exceptions in case of unrepresentable text data, the encoding argument should be specified as “utf-8”. So what happens if you're not explicit about the encoding, i.e. just doc.toprettyxml()? This would hopefully at least move your exception to a more appropriate place. In any case, one solution would be to scrub the string in your content variable to get rid of the invalid characters (hopefully they're insignificant). Maybe something like this: def unicode_filter(char): try: unicode(char, encoding='utf-8', errors='strict') return char except UnicodeDecodeError: return '' content = 'abc\xFF' content = ''.join(map(unicode_filter, content)) print content Not really my area of expertise, but maybe worth a shot -Jon 1. http://docs.python.org/2/library/xml.dom.minidom.html#xml.dom.minidom.Node.toxml -- Jon Stroop Digital Initiatives Programmer/Analyst Princeton University Library jstr...@princeton.edu On 03/04/2013 03:00 PM, Michael Beccaria wrote: I'm working on a project that takes the ocr data found in a pdf and places it in a custom xml file. I use Python scripts to create the xml file. Something like this (trimmed down a bit): from xml.dom.minidom import Document doc = Document() Page = doc.createElement(Page) doc.appendChild(Page) f = StringIO(txt) lines = f.readlines() for line in lines: word = doc.createElement(String) ... word.setAttribute(CONTENT,content) Page.appendChild(word) return doc.toprettyxml(indent= ,encoding=utf-8) This creates a file, simply, that looks like this: ?xml version=1.0 encoding=utf-8? Page HEIGHT=3296 WIDTH=2609 String CONTENT=BuffaloLaunch / String CONTENT=Club / String CONTENT=Offices / String CONTENT=Installed / ... /Page I am able to get this document to be created ok and saved to an xml file. The problem occurs when I try and have it read using the lxml library: from lxml import etree doc = etree.parse(filename) I am running across errors like XMLSyntaxError: Char 0x out of allowed range, line 94, column 19. Which when I look at the file, is true. There is a 0X character in the content field. How is a file able to be created using minidom (which I assume would create a valid xml file) and then failing when parsing with lxml? What should I do to fix this on the encoding side so that errors don't show up on the parsing side? Thanks, Mike How is the Mike Beccaria Systems Librarian Head of Digital Initiative Paul Smith's College 518.327.6376 mbecca...@paulsmiths.edu Become a friend of Paul Smith's Library on Facebook today!
Re: [CODE4LIB] XML Parsing and Python
I'll note that 0x is a UTF-8 non-character, and these noncharacters should never be included in text interchange between implementations. [1] I assume the OCR engine maybe using 0x when it can't recognize a character? So, it's not wrong for a parser to complain (or, not complain) about 0x, and you can just scrub the string like Jon suggests. Chris [1] http://en.wikipedia.org/wiki/Mapping_of_Unicode_characters#Noncharacters On 5 Mar, 2013, at 9:16 , Jon Stroop jstr...@princeton.edu wrote: Mike, I haven't used minidom extensively but my guess is that doc.toprettyxml(indent= ,encoding=utf-8) isn't actually changing the encoding because it can't parse the string in your content variable. I'm surprised that you're not getting tossed a UnicodeError, but The docs for Node.toxml() [1] might shed some light: To avoid UnicodeError exceptions in case of unrepresentable text data, the encoding argument should be specified as “utf-8”. So what happens if you're not explicit about the encoding, i.e. just doc.toprettyxml()? This would hopefully at least move your exception to a more appropriate place. In any case, one solution would be to scrub the string in your content variable to get rid of the invalid characters (hopefully they're insignificant). Maybe something like this: def unicode_filter(char): try: unicode(char, encoding='utf-8', errors='strict') return char except UnicodeDecodeError: return '' content = 'abc\xFF' content = ''.join(map(unicode_filter, content)) print content Not really my area of expertise, but maybe worth a shot -Jon 1. http://docs.python.org/2/library/xml.dom.minidom.html#xml.dom.minidom.Node.toxml -- Jon Stroop Digital Initiatives Programmer/Analyst Princeton University Library jstr...@princeton.edu On 03/04/2013 03:00 PM, Michael Beccaria wrote: I'm working on a project that takes the ocr data found in a pdf and places it in a custom xml file. I use Python scripts to create the xml file. Something like this (trimmed down a bit): from xml.dom.minidom import Document doc = Document() Page = doc.createElement(Page) doc.appendChild(Page) f = StringIO(txt) lines = f.readlines() for line in lines: word = doc.createElement(String) ... word.setAttribute(CONTENT,content) Page.appendChild(word) return doc.toprettyxml(indent= ,encoding=utf-8) This creates a file, simply, that looks like this: ?xml version=1.0 encoding=utf-8? Page HEIGHT=3296 WIDTH=2609 String CONTENT=BuffaloLaunch / String CONTENT=Club / String CONTENT=Offices / String CONTENT=Installed / ... /Page I am able to get this document to be created ok and saved to an xml file. The problem occurs when I try and have it read using the lxml library: from lxml import etree doc = etree.parse(filename) I am running across errors like XMLSyntaxError: Char 0x out of allowed range, line 94, column 19. Which when I look at the file, is true. There is a 0X character in the content field. How is a file able to be created using minidom (which I assume would create a valid xml file) and then failing when parsing with lxml? What should I do to fix this on the encoding side so that errors don't show up on the parsing side? Thanks, Mike How is the Mike Beccaria Systems Librarian Head of Digital Initiative Paul Smith's College 518.327.6376 mbecca...@paulsmiths.edu Become a friend of Paul Smith's Library on Facebook today!
Re: [CODE4LIB] XML Parsing and Python
It sounds like your code isn't recognizing the XML file as UTF-8 (even though the encoding is correctly marked in your example). You could try telling the parser explicitly to use UTF-8, like this parser = XMLParser(encoding=utf-8) As discussed in http://www.daniweb.com/software-development/python/threads/435360/using-xml.etree-with-xml-files-containing-a-symbol There's also a bit of discussion about using lxml to parse UTF-8 in http://stackoverflow.com/questions/3402520/is-there-a-way-to-force-lxml-to-parse-unicode-strings-that-specify-an-encoding-i Hope this helps! Regards, Stuart On Mon, Mar 4, 2013 at 3:00 PM, Michael Beccaria mbecca...@paulsmiths.eduwrote: I'm working on a project that takes the ocr data found in a pdf and places it in a custom xml file. I use Python scripts to create the xml file. Something like this (trimmed down a bit): from xml.dom.minidom import Document doc = Document() Page = doc.createElement(Page) doc.appendChild(Page) f = StringIO(txt) lines = f.readlines() for line in lines: word = doc.createElement(String) ... word.setAttribute(CONTENT,content) Page.appendChild(word) return doc.toprettyxml(indent= ,encoding=utf-8) This creates a file, simply, that looks like this: ?xml version=1.0 encoding=utf-8? Page HEIGHT=3296 WIDTH=2609 String CONTENT=BuffaloLaunch / String CONTENT=Club / String CONTENT=Offices / String CONTENT=Installed / ... /Page I am able to get this document to be created ok and saved to an xml file. The problem occurs when I try and have it read using the lxml library: from lxml import etree doc = etree.parse(filename) I am running across errors like XMLSyntaxError: Char 0x out of allowed range, line 94, column 19. Which when I look at the file, is true. There is a 0X character in the content field. How is a file able to be created using minidom (which I assume would create a valid xml file) and then failing when parsing with lxml? What should I do to fix this on the encoding side so that errors don't show up on the parsing side? Thanks, Mike How is the Mike Beccaria Systems Librarian Head of Digital Initiative Paul Smith's College 518.327.6376 mbecca...@paulsmiths.edu Become a friend of Paul Smith's Library on Facebook today!
