[BioRuby] Bio::PubMed.efetch, bug?

Masahide Kikkawa mkikkawa at gmail.com
Fri Apr 10 07:20:19 UTC 2009


  I recently installed bioruby-1.3.0 and encountered a bug.

Here is what I did
result = Bio::PubMed.efetch([123,456,789])

I expected the result to be Array of MEDLINE formatted String
as documented here:

However, the return value was one String containing all the results.

In the bioruby-1.2.1, it does return Array of MEDLINE formatted String.

Therefore I would recommend to apply following patch to ncbirest.rb

<     result.strip!
<     if opts["retmode"] == "text"
<       result = result.split(/\n\n+/)
<     end
<     return result
 >     return result.strip
 >     #return result.strip.split(/\n\n+/)

Masahide Kikkawa, M.D., Ph. D.
Structural Biology
Graduate School of Science
Kyoto University
Oiwake, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502
Tel: +81-75-753-9421
FAX: +81-75-753-4218

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