[BioRuby] biofetch confusion
Ben Woodcroft
donttrustben at gmail.com
Tue Sep 30 02:40:39 UTC 2008
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
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