[Bioperl-l] BLASTXML XML::SAX::Expat issues resolved

Chris Fields cjfields at uiuc.edu
Tue Jan 30 14:47:55 EST 2007


Sendu, all,

Björn Höhrmann updated XML::SAX::Expat to v0.38 on CPAN to fix a bug  
that was killing BLAST XML parsing, so XML::SAX::Expat now works with  
BLASTXML parsing.  However, it still has some problems with character  
encoding.  This bug only seems to affect the output from description 
() due to '>'.  Beyond that, every backend parser (XML::SAX::Expat,  
XML::SAX::ExpatXS) works and passes tests, even with XML::SAX  
character encoding issues.  I am still waiting to hear back from  
Grant McLean on progress in fixing that particular XML::SAX bug.

Based on that I think we can remove any absolute ExpatXS requirement  
(we can just require XML::SAX), though I still strongly recommend  
using XML::SAX::ExpatXS or XML::LibXML::SAX::Parser.  A warning is in  
place to warn users about entities issues if one uses an affected  
XML::SAX backend (XML::SAX::PurePerl, XML::LibXML::SAX,  
XML::SAX::Expat).

cheers!

chris


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