[BioRuby-cvs] bioruby/lib/bio reference.rb,1.24.2.6,1.24.2.7

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv20065/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	reference.rb 
Log Message:
merged changes in trunk (revision 1.30)


Index: reference.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/reference.rb,v
retrieving revision 1.24.2.6
retrieving revision 1.24.2.7
diff -C2 -d -r1.24.2.6 -r1.24.2.7
*** reference.rb	23 Apr 2008 18:52:18 -0000	1.24.2.6
--- reference.rb	17 Jun 2008 12:23:49 -0000	1.24.2.7
***************
*** 180,186 ****
      # *Arguments*:
      # * (optional) _style_: String with style identifier
!     # * (optional) _option_: Option for styles accepting one
      # *Returns*:: String
!     def format(style = nil, option = nil)
        case style
        when 'embl'
--- 180,186 ----
      # *Arguments*:
      # * (optional) _style_: String with style identifier
!     # * (optional) _options_: Options for styles accepting one
      # *Returns*:: String
!     def format(style = nil, *options)
        case style
        when 'embl'
***************
*** 189,199 ****
          return endnote
        when 'bibitem'
!         return bibitem(option)
        when 'bibtex'
!         return bibtex(option)
        when 'rd'
!         return rd(option)
        when /^nature$/i
!         return nature(option)
        when /^science$/i
          return science
--- 189,199 ----
          return endnote
        when 'bibitem'
!         return bibitem(*options)
        when 'bibtex'
!         return bibtex(*options)
        when 'rd'
!         return rd(*options)
        when /^nature$/i
!         return nature(*options)
        when /^science$/i
          return science
***************
*** 247,256 ****
        lines << "%P #{@pages}" unless @pages.empty?
        lines << "%M #{@pubmed}" unless @pubmed.to_s.empty?
!       if @pubmed
!         cgi = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
!         opts = "cmd=Retrieve&db=PubMed&dopt=Citation&list_uids"
!         @url = "#{cgi}?#{opts}=#{@pubmed}"
!       end
!       lines << "%U #{@url}" unless @url.empty?
        lines << "%X #{@abstract}" unless @abstract.empty?
        @mesh.each do |term|
--- 247,252 ----
        lines << "%P #{@pages}" unless @pages.empty?
        lines << "%M #{@pubmed}" unless @pubmed.to_s.empty?
!       u = @url.empty? ? pubmed_url : @url
!       lines << "%U #{u}" unless u.empty?
        lines << "%X #{@abstract}" unless @abstract.empty?
        @mesh.each do |term|
***************
*** 289,292 ****
--- 285,290 ----
      #     {\em Theor. J. Hoge}, 12(3):123--145, 2001.
      # ---
+     # *Arguments*:
+     # * (optional) _item_: label string (default: <tt>"PMID:#{pubmed}"</tt>).
      # *Returns*:: String
      def bibitem(item = nil)
***************
*** 332,351 ****
      # *Arguments*:
      # * (optional) _section_: BiBTeX section as String
      # *Returns*:: String
!     def bibtex(section = nil)
        section = "article" unless section
        authors = authors_join(' and ', ' and ')
!       pages   = @pages.sub('-', '--')
!       return <<-"END".gsub(/\t/, '')
!         @#{section}{PMID:#{@pubmed},
!           author  = {#{authors}},
!           title   = {#{@title}},
!           journal = {#{@journal}},
!           year    = {#{@year}},
!           volume  = {#{@volume}},
!           number  = {#{@issue}},
!           pages   = {#{pages}},
!         }
!       END
      end
  
--- 330,375 ----
      # *Arguments*:
      # * (optional) _section_: BiBTeX section as String
+     # * (optional) _label_: Label string cited by LaTeX documents.
+     #                       Default is <tt>"PMID:#{pubmed}"</tt>.
+     # * (optional) _keywords_: Hash of additional keywords,
+     #                          e.g. { 'abstract' => 'This is abstract.' }.
+     #                          You can also override default keywords.
+     #                          To disable default keywords, specify false as
+     #                          value, e.g. { 'url' => false, 'year' => false }.
      # *Returns*:: String
!     def bibtex(section = nil, label = nil, keywords = {})
        section = "article" unless section
        authors = authors_join(' and ', ' and ')
!       thepages = pages.to_s.empty? ? nil : pages.sub(/\-/, '--')
!       unless label then
!         label = "PMID:#{pubmed}"
!       end
!       theurl = if !(url.to_s.empty?) then
!                  url
!                elsif pmurl = pubmed_url and !(pmurl.to_s.empty?) then
!                  pmurl
!                else
!                  nil
!                end
!       hash = {
!         'author'  => authors.empty?    ? nil : authors,
!         'title'   => title.to_s.empty? ? nil : title,
!         'number'  => issue.to_s.empty? ? nil : issue,
!         'pages'   => thepages,
!         'url'     => theurl
!       }
!       keys = %w( author title journal year volume number pages url )
!       keys.each do |k|
!         hash[k] = self.__send__(k.intern) unless hash.has_key?(k)
!       end
!       hash.merge!(keywords) { |k, v1, v2| v2.nil? ? v1 : v2 }
!       bib = [ "@#{section}{#{label}," ]
!       keys.concat((hash.keys - keys).sort)
!       keys.each do |kw|
!         ref = hash[kw]
!         bib.push "  #{kw.ljust(12)} = {#{ref}}," if ref
!       end
!       bib.push "}\n"
!       return bib.join("\n")
      end
  
***************
*** 533,536 ****
--- 557,571 ----
      end
  
+     # Returns a valid URL for pubmed records
+     #
+     # *Returns*:: String
+     def pubmed_url
+       unless @pubmed.to_s.empty?
+         cgi = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
+         opts = "cmd=Retrieve&db=PubMed&dopt=Citation&list_uids"
+         return "#{cgi}?#{opts}=#{@pubmed}"
+       end
+       ''
+     end
  
      private