[BioRuby] Porting PhyloXML to Nokogiri, maybe repackaging it

[Raoul Bonnal]

Impressive.
This is the right approach for cleaning BioRuby from dependencies which
could create problems.


Thanks Clayton.


On 16/05/12 10.17, "Naohisa GOTO" <ngoto at gen-info.osaka-u.ac.jp> wrote:

> Hi,
> 
> Great work, Clayton!
> 
> I think separate gem (Biogem) is good, too.
> 
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> 
> On Tue, 15 May 2012 20:54:32 +0200
> Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> 
>> Marvellous work Clayton! My suggestion to BioRuby is to split out
>> phyloxml and to deprecate the current library module. In the next
>> release, or after, we should take out that code. I suspect few people
>> really depend on it, and they can adapt. I am partly responsible for
>> that dependency, and I think the Travis-ci tests also point out that
>> the purer Ruby BioRuby is, the better ;).
>> 
>> Naohisa, what do you say? We should also ask the original author, even
>> though she has left our little group and now works for google (and I
>> am claiming Google does not recruit from GSoC :). Diana, maybe you are
>> reading the ML?
>> 
>> Pj.
>> 
>> On Tue, May 15, 2012 at 01:08:20PM -0400, Clayton Wheeler wrote:
>>> Hi all,
>>> 
>>> The PhyloXML unit tests are failing under JRuby, because the libxml-jruby
>>> gem (an implementation of the libxml API using native Java XML libraries)
>>> does not support the full API of libxml-ruby. My first approach to this was
>>> to simply use the native libxml-ruby gem and its C extension, which works
>>> with JRuby in 1.8 mode. However, it doesn't work in 1.9 mode due to a
>>> Unicode issue, and the JRuby developers indicate that the C extension API
>>> (as opposed to FFI, I suppose) isn't likely to be supported further in 1.9
>>> mode. (see http://bit.ly/JGWC4K)
>>> 
>>> There was a discussion of the PhyloXML parser on the mailing list a couple
>>> of months ago (http://bit.ly/JFX8Qf), and Naohisa indicated that it might be
>>> rewritten to use Nokogiri at some point soon, since Nokogiri is now the de
>>> facto standard XML parser. Following that lead, I've gone ahead and ported
>>> the PhyloXML parser to use Nokogiri; it only took an hour or two, and the
>>> unit tests are passing. My branch for this is at
>>> https://github.com/csw/bioruby/tree/phyloxml-nokogiri. If this seems like a
>>> good approach, I can port the writer as well.
>>> 
>>> However, Pjotr suggested that it might make sense to split PhyloXML out into
>>> a separate gem. This should be straightforward enough, since no other
>>> BioRuby components appear to call PhyloXML. It would mean that any PhyloXML
>>> users would need to install a separate gem. On the other hand, it would
>>> remove a dependency on libxml2 for core BioRuby on MRI. Thoughts? Should I
>>> proceed with this approach?
>>> 
>>> Clayton Wheeler
>>> cswh at umich.edu
>>> 
>>> 
>>> _______________________________________________
>>> BioRuby Project - http://www.bioruby.org/
>>> BioRuby mailing list
>>> BioRuby at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>> 
>> _______________________________________________
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> 
> 
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