[Bioperl-l] Re: bad entries in interpro again

[Hilmar Lapp]

This sounds more like an expat or XML::Parser problem. Have you tried 
to upgrade either? Maybe check with the authors of those modules?

	-hilmar

On Dec 2, 2004, at 2:11 AM, Mikko Arvas wrote:

>
> Hi,
>
> At 13:49 1.12.2004 -0800, Hilmar Lapp wrote:
>
>> On Wednesday, December 1, 2004, at 08:16  AM, Mikko Arvas wrote:
>>
>>> Is the &apos the source of the problem?
>> Did you try to take it out and see what happens? I.e., you can answer 
>> this yourself easily.
>> I would have thought that it's not the problem, but it'd be great if 
>> you or somebody else helps out by testing what was suggested.
>
> Sorry about that I should have tested it before mailing. The problem 
> is not non-ascii characters it seems to be specifically the 
> combination of two & inside individual <>. I tried various 
> combinations and other non-ascii characters (even in abundance) don't 
> break it and a single & does neither.
>
> Here is again the problematic line:
> <interpro id="IPR002073" name="3&apos;5&apos;-cyclic nucleotide 
> phosphodiesterase" type="Domain" parent_id="IPR003607">
>
> And its error:
> not well-formed (invalid token) at line 2, column 54, byte 132 at  
> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/XML/Parser.pm
> line 187
>
> So which way to proceed?
>
>>> Is it really a problem in BioPerl or in expat?
>>
>> If the problem is outside of Interpro, it's Expat, not Bioperl. It's 
>> the XML parser library that threw up.
>>
>>>  Is somebody trying to solve the problem for Bioperl now
>>> and is there any sensible thing that the interpro team could do to 
>>> help?
>>
>> Depends on where the problem is. It appears that the Interpro team 
>> already eliminated the double quotes in names. The is some hard-coded 
>> stuff in interpro.pm that needs to be removed,  and I heard Allen say 
>> he'll work on that.
>>
>>         -hilmar
>
> Cheers,
> mikko
>
>
>
> Mikko Arvas
> VTT Biotechnology
>
> e-mail:            mikko.arvas at vtt.fi
> tel:                 +358-(0)9-456 5827
> mobile:           +358-(0)44-381 0502
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> mail:               Tietotie 2, Espoo
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>                       FIN-02044 VTT, Finland
>
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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