[BioRuby-cvs] bioruby/lib/bio/io pubmed.rb,1.18,1.19

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv6745/io

Modified Files:
	pubmed.rb 
Log Message:
* esearch2, efetch2: candidates for the better replacement of esearch and efetch methods which are enchanced to accept options as a hash and utilize Bio::Command.post_form for the options


Index: pubmed.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/pubmed.rb,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** pubmed.rb	10 Nov 2007 08:21:54 -0000	1.18
--- pubmed.rb	15 Nov 2007 07:23:39 -0000	1.19
***************
*** 9,15 ****
  #
  
- require 'net/http'
- require 'cgi' unless defined?(CGI)
  require 'bio/command'
  
  module Bio
--- 9,14 ----
  #
  
  require 'bio/command'
+ require 'cgi' unless defined?(CGI)
  
  module Bio
***************
*** 112,115 ****
--- 111,134 ----
    end
  
+   def self.esearch2(str, hash = {})
+     serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
+     opts = {
+       "retmax" => 100,
+       "tool"   => "bioruby",
+       "db"     => "pubmed",
+       "term"   => str
+     }
+     opts.update(hash)
+ 
+     response, = Bio::Command.post_form(serv, opts)
+     result = response.body
+     if opts['rettype'] == 'count'
+       result = result.scan(/<Count>(.*?)<\/Count>/m).flatten.first.to_i
+     else
+       result = result.scan(/<Id>(.*?)<\/Id>/m).flatten
+     end
+     return result
+   end
+ 
    # Retrieve PubMed entry by PMID and returns MEDLINE formatted string using
    # entrez efetch. Multiple PubMed IDs can be provided:
***************
*** 132,136 ****
      response, = http.get(path + list)
      result = response.body
!     result = result.split(/\n\n+/)
      return result
    end
--- 151,173 ----
      response, = http.get(path + list)
      result = response.body
!     return result
!   end
! 
!   def self.efetch2(ids, hash = {})
!     return "" if ids.empty?
!     ids = ids.join(",") if ids === Array
! 
!     serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
!     opts = {
!       "tool"     => "bioruby",
!       "db"       => "pubmed",
!       "retmode"  => "text",
!       "rettype"  => "medline",
!       "id"       => ids,
!     }
!     opts.update(hash)
! 
!     response, = Bio::Command.post_form(serv, opts)
!     result = response.body
      return result
    end
***************
*** 212,216 ****
  
    puts "--- Search PubMed by E-Utils ---"
!   Bio::PubMed.esearch("(genome AND analysis) OR bioinformatics)").each do |x|
      p x
    end
--- 249,255 ----
  
    puts "--- Search PubMed by E-Utils ---"
!   puts Bio::PubMed.esearch("(genome AND analysis) OR bioinformatics)", {"rettype" => "count"})
! 
!   Bio::PubMed.esearch2("(genome AND analysis) OR bioinformatics)").each do |x|
      p x
    end
***************
*** 218,221 ****
--- 257,261 ----
    puts "--- Retrieve PubMed entry by E-Utils ---"
    puts Bio::PubMed.efetch("10592173", "14693808")
+   puts Bio::PubMed.efetch2(["10592173", "14693808"], {"retmode" => "xml"})
  
    puts "--- Search PubMed by Entrez CGI ---"