[Bioperl-l] XML parser preference?

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Thu Aug 10 13:25:58 EDT 2006


As long as we don't complicate things for new users, picking those 
parsers is fine for me. Thanks Jurgen (and Rutger) for giving us advice 
on libxml2's availability :)

Mauricio.

Chris Fields wrote:
> Jurgen,
> 
> Thanks for pointing that out!  However, the problem is we want to  
> keep the number of dependencies down; there are already four XML  
> parser dependencies for Bioperl (XML::Twig is one, but XML::LibXML  
> isn't).
> 
> Maybe new modules which require XML parsing stick with four XML  
> parsers.  However, not the current four (XML::DOM, XML::Twig,   
> XML::Parser, XML::SAX).
> 
> Maybe we should pick four XML parsers, each with their own particular  
> strengths:
> 
> 1)  XML::SAX  (SAX parsing; flexible, can use pure Perl, ExpatXS, etc)
>       Switch using XML::Parser to XML::SAX (done for  
> Bio::SeacrhIO::blastxml)
> 2)  XML::LibXML (DOM parsing; maintained, up to date, fast)
>      Switch using XML::DOM to XML::LibXML
> 3)  XML::Twig (DOM-like, SAX-based) - great for processing 'chunks'  
> of XML
>       Used in Bio::DB::Taxonomy::entrez
> 4)  XML::Simple (small XML) - very easy to use XML parser
> 
> Since they are currently available for most (all?) OS's, shouldn't be  
> a problem.  What do you think Mauricio?
> 
> Chris
> 
> 
> On Aug 10, 2006, at 7:29 AM, Jurgen Pletinckx wrote:
> 
>> | I have no doubt that XML::LibXML is a great parser (I've used
>> | it a few
>> | times), the problem with it is that it runs on top of libxml2's C
>> | library. On *nix systems it's fairly simple to have this dependency
>> | compiled and running, but what about having it under other OS's
>> (e.g.
>> | Windows)?
>> |
>> | Introducing XML::LibXML as a dependency into the toolkit will
>> | probably
>> | place EUtilities as a module not usable by everyone, especially
>> those
>> | who use BioPerl in a OS where installing/compiling C
>> | dependencies can be
>> | a headache.
>>
>> Regarding XML::LibXML, there does appear to be an up-to-date ppm
>> package (which fetches libxml2.dll) at
>>
>> http://theoryx5.uwinnipeg.ca/ppms/XML-LibXML.ppd
>>
>> (and less than a week since the release of the corresponding
>> version to cpan, too.)
>>
>> So the threshold for distribution to Windows, at least, is less
>> high than it might have been.
>>
>> -- 
>> Jurgen Pletinckx
>> AlgoNomics NV
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
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> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM



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