[BioRuby] Bio::Fetch issue - biofetch.rb not found

[Naohisa GOTO]

Hi,

The issue is marked as a bug in the OBF Redmine.

https://redmine.open-bio.org/issues/3294

Thanks,

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

On Thu, 22 Sep 2011 15:12:07 +0900
Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:

> Hello Marc,
> 
> Sorry for late response.
> 
> > http://bioruby.org/cgi-bin/biofetch.rb - which does not seem to exist at 
> > that location?
> 
> The service is down for years, due to the server trouble,
> and it is currently difficult to restore the service
> because of the internal structure of bioruby.org.
> 
> Please use other server, e.g.
> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
> 
>  bf =Bio::Fetch.new('http://www.ebi.ac.uk/Tools/dbfetch/dbfetch')
>  str = bf.fetch('embl', 'AE014292')
>  print str
> 
> Alternatively, some other classes provide similar function.
> 
>  str = Bio::TogoWS::REST.entry('genbank', 'AF237819')
>  print str
> 
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
> 
> On Mon, 19 Sep 2011 10:57:14 +0200
> "Marc P. Hoeppner" <mphoeppner at gmail.com> wrote:
> 
> > Hi,
> > 
> > when trying to fetch entries from remote databases via Bio::Fetch, I 
> > receive the following error:
> > 
> > /usr/lib/ruby/1.8/open-uri.rb:277:in `open_http': 404 Not Found 
> > (OpenURI::HTTPError)
> > 
> > It appears the default entry for Fetch.new searches for 
> > http://bioruby.org/cgi-bin/biofetch.rb - which does not seem to exist at 
> > that location?
> > 
> > Am I doing anything wrong?
> > 
> > Using gem version 1.4.2 and ruby 1.8.7 on Ubuntu 11.04
> > 
> > /Marc
> > _______________________________________________
> > 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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