[BioRuby] biofetch confusion

[Toshiaki Katayama]

Hi,

> Should bioruby add the http:// somehow?

I don't think so. Please add protocol prefix by yourself.

Toshiaki

On 2008/09/30, at 11:40, Ben Woodcroft wrote:

> Hi,
>
> I was running a fetch from within ruby using the alternate server, and ran
> into a problem it took stupid me a little while to figure out. Thought I
> might post to help others.
>
>>> pdb = Bio::Fetch.new('www.ebi.ac.uk/cgi-bin/dbfetch').fetch('pdb','2A06')
> NoMethodError: You have a nil object when you didn't expect it!
> The error occurred while evaluating nil.downcase
>    from /usr/lib/ruby/1.8/open-uri.rb:551:in `find_proxy'
>    from /usr/lib/ruby/1.8/open-uri.rb:147:in `open_loop'
>    from /usr/lib/ruby/1.8/open-uri.rb:164:in `call'
>    from /usr/lib/ruby/1.8/open-uri.rb:164:in `open_loop'
>    from /usr/lib/ruby/1.8/open-uri.rb:162:in `catch'
>    from /usr/lib/ruby/1.8/open-uri.rb:162:in `open_loop'
>    from /usr/lib/ruby/1.8/open-uri.rb:132:in `open_uri'
>    from /home/ben/forays/bioruby_wwood/lib/bio/command.rb:223:in `read_uri'
>    from /home/ben/forays/bioruby_wwood/lib/bio/io/fetch.rb:109:in `fetch'
>    from (irb):5
>
>
> Same problem happens when you use the br_biofetch.rb script directly.
>
>
> The problem was fixed by adding 'http://' to the front of the url:
>
>>> pdb = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch').fetch('pdb
> ','2A06')
> ... pdb printed here ...
>
>
> Should bioruby add the http:// somehow?
>
> Thanks,
> ben
>
> -- 
> FYI: My email addresses at unimelb, uq and gmail all redirect to the same
> place.
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