[BioRuby] KEGG API

[Naohisa Goto]

Hi,

It is reproduced with SOAP4R 1.5.8, the latest release version of SOAP4R.
It can not be reproduced with SOAP4R 1.5.5 bundled with Ruby 1.8.7-p299.

>From the revision 1683 of SOAP4R, it does not add mappings for already
defined methods.
http://dev.ctor.org/soap4r/changeset/1683

In Debian (and Ubuntu) package version of Ruby 1.8.7, the patch is
applied to prevent memory exhaust problem as a security fix.

The workaround is to use SOAP::Mapping::Object#[].
For example, use rel["type"] instead of rel.type.

  api = Bio::KEGG::API.new
  relations = api.get_element_relations_by_pathway('path:bsu00010')
  relations.each do |rel|
    puts rel.element_id1
    puts rel.element_id2
    puts rel["type"]
    rel.subtypes.each do |sub|
      puts sub.element_id
      puts sub.relation
      puts sub["type"]
    end
  end

> Dear All
> 
> I have a question about KEGG API on BioRuby.
> When I use "type" method, "deprecated" message was returned.
> While, the method "type" is still working, refer to KEGG manual.
> 
> ## Script I used is below
> 
> relations = get_element_relations_by_
> pathway('path:bsu00010')
> relations.each do |rel|
>   puts rel.element_id1
>    puts rel.element_id2
>    puts rel.type
>    rel.subtypes.each do |sub|
>      puts sub.element_id
>      puts sub.relation
>      puts sub.type
>    end
> end
> 
> Result for sub.type => "sub.type was deprecated use class"
> 
> 
> How can I receive type property in the class
> "get_element_relations_by_pathway" ?
> 
> With best wishes,
> 
> Daiji Endoh
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

-- 
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org