Re: cleaning up an ASCII file?
- From: Nick Matzke <matzke@xxxxxxxxxxxx>
- Date: Wed, 10 Jun 2009 17:52:09 -0700
Apologies, I figured there was some easy, obvious solution, since there is in BBedit. I will explain further...
John Machin wrote:
On Jun 11, 6:09 am, Nick Matzke <mat...@xxxxxxxxxxxx> wrote:Hi all,
So I'm parsing an XML file returned from a database. However, the
database entries have occasional non-ASCII characters, and this is
crashing my parsers.
So fix your parsers. google("unicode"). Deleting stuff that you don't
understand is an "interesting" approach to academic research :-(
Not if it's just weird versions of dash characters and umlauted characters the like, which is what I bet it is. Those sorts of things and the apparent inability of lots of email readers and websites to deal with them have been annoying me for years, so I tend to move straight towards genocidal tactics when I detect their presence.
(My database source is GBIF, they get museum specimen submissions from around the planet, there are zillions of records, I am just a user, so fixing it on their end is not a realistic option.)
Care to divulge what "crash" means? e.g. the full traceback and error
message, plus what version of python on what platform, what version of
ElementTree or other XML spftware you are using ...
All that is fine, the problem is actually when I try to print to screen in IPython:
============
UnicodeEncodeError: 'ascii' codec can't encode character u'\xe4' in position 293: ordinal not in range(128)
============
Probably this is the line in the file which is causing problems (as displayed in BBedit):
======================
<gbif:statements>-
This document contains data shared through the GBIF Network - see http://data.gbif.org/ for more information.
All usage of these data must be in accordance with the GBIF Data Use Agreement - see http://www.gbif.org/DataProviders/Agreements/DUA
Please cite these data as follows:
Jyväskylä University Museum - The Section of Natural Sciences, Vascular plant collection of Jyvaskyla University Museum (accessed through GBIF data portal, http://data.gbif.org/datasets/resource/462, 2009-06-11)
Missouri Botanical Garden, Missouri Botanical Garden (accessed through GBIF data portal, http://data.gbif.org/datasets/resource/621, 2009-06-11)
Museo Nacional de Costa Rica, herbario (accessed through GBIF data portal, http://data.gbif.org/datasets/resource/566, 2009-06-11)
National Science Museum, Japan, Kurashiki Museum of Natural History (accessed through GBIF data portal, http://data.gbif.org/datasets/resource/599, 2009-06-11)
The Swedish Museum of Natural History (NRM), Herbarium of Oskarshamn (OHN) (accessed through GBIF data portal, http://data.gbif.org/datasets/resource/1024, 2009-06-11)
Tiroler Landesmuseum Ferdinandeum, Tiroler Landesmuseum Ferdinandeum (accessed through GBIF data portal, http://data.gbif.org/datasets/resource/1509, 2009-06-11)
UCD, Database Schema for UC Davis [Herbarium Labels] (accessed through GBIF data portal, http://data.gbif.org/datasets/resource/734, 2009-06-11)
-
</gbif:statements>
======================
Presumably "Jyväskylä University Museum" is the problem since there are umlauted a's in there. (Note, though, that I have thousands of records to parse, so there is going to be all kinds of other umlauted & accented stuff in these sorts of search results.
So the goal is to replace the characters with un-umlauted versions or some such.
Cheers!
Nick
PS: versions I am using:
========
nick$ python -V
Python 2.5.2 |EPD Py25 4.1.30101|
========
Center for Theoretical Evolutionary Genomics
If your .sig evolves much more, it will consume all available
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....its easier to have a big sig than to try and remember all that stuff ;-)...
--
====================================================
Nicholas J. Matzke
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Huelsenbeck Lab
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-----------------------------------------------------
"[W]hen people thought the earth was flat, they were wrong. When people thought the earth was spherical, they were wrong. But if you think that thinking the earth is spherical is just as wrong as thinking the earth is flat, then your view is wronger than both of them put together."
Isaac Asimov (1989). "The Relativity of Wrong." The Skeptical Inquirer, 14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
====================================================
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