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

[Naohisa GOTO]

Hi,

On Fri, 10 Apr 2009 16:20:19 +0900
Masahide Kikkawa <mkikkawa at gmail.com> wrote:

> Hi,
> 
> 
>   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:
> http://bioruby.org/rdoc/classes/Bio/PubMed.html
> 
> 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.

Thank you for reporting a bug. This is a regression introduced
with the refactoring of Bio::PubMed between 1.2.1 and 1.3.0.

> 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+/)
> 

Bio::NCBI::REST is not only for PubMed but also for many
databases in NCBI, and efetch may return free text,
depending on databases. Thus, the processing of the result
should only be applied to Bio::PubMed.

http://github.com/bioruby/bioruby/commit/a48a9a35b87dead069fe328ba7086977304af995

To confirm bug fix, tests for Bio::PubMed are also added.

http://github.com/bioruby/bioruby/commit/bf5ba6d4503f3ddb0ca31673882f5b396a932bbe

In addition, I found a bug about "retstart" and fixed the bug.

http://github.com/bioruby/bioruby/commit/fc0339fe8a42cd00199cfdc938590ae9626551bc


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