[BioRuby-cvs] bioruby/test/unit/bio test_reference.rb,NONE,1.1

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory pub.open-bio.org:/tmp/cvs-serv12435/test/unit/bio

Added Files:
	test_reference.rb 
Log Message:
* lib/bio/reference.rb: fixed a bug in the endnote method.
* test/unit/bio/test_reference.rb: newly added.


--- NEW FILE: test_reference.rb ---
#
# = test/bio/tc_pathway.rb - Unit test for Bio::Pathway
#
# Copyright::  Copyright (C) 2006 
#              Mitsuteru C. Nakao <n at bioruby.org>
# Lisence::    Ruby's
#
# $Id: test_reference.rb,v 1.1 2006/02/08 15:06:26 nakao Exp $
#

require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), [".."] * 3, "lib")).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)

require 'test/unit'
require 'bio/reference'


module Bio
  class TestReference < Test::Unit::TestCase
    
    def setup
      hash = {'authors' => [ "Hoge, J.P.", "Fuga, F.B." ], 'title' => "Title of the study.",
              'journal' => "Theor. J. Hoge", 'volume' => 12, 'issue' => 3, 'pages' => "123-145",
              'year' => 2001, 'pubmed' => 12345678, 'medline' => 98765432, 'abstract' => "Hoge fuga. hoge fuga.",
              'url' => "http://example.com", 'mesh' => ['Hoge'], 'affiliations' => ['Tokyo']}
      @obj = Bio::Reference.new(hash)
    end

    def test_authors
      ary = [ "Hoge, J.P.", "Fuga, F.B." ]
      assert_equal(ary, @obj.authors)
    end

    def test_journal
      str = 'Theor. J. Hoge'
      assert_equal(str, @obj.journal)      
    end
    
    def test_volume
      str = 12
      assert_equal(str, @obj.volume)      
    end

    def test_issue
      str = 3
      assert_equal(str, @obj.issue)      
    end

    def test_pages
      str = '123-145'
      assert_equal(str, @obj.pages)
    end

    def test_year
      str = 2001
      assert_equal(str, @obj.year)
    end
    
    def test_pubmed
      str = 12345678
      assert_equal(str, @obj.pubmed)
    end

    def test_abstract
      str = 'Hoge fuga. hoge fuga.'
      assert_equal(str, @obj.abstract)
    end

    def test_url
      str = 'http://example.com'
      assert_equal(str, @obj.url)
    end

    def test_mesh
      str = ['Hoge']
      assert_equal(str, @obj.mesh)
    end

    def test_affiliations
      str = ['Tokyo']
      assert_equal(str, @obj.affiliations)
    end

    def test_format_general
      str = 'Hoge, J.P., Fuga, F.B. (2001). "Title of the study." Theor. J. Hoge 12:123-145.'
      assert_equal(str, @obj.format)
      assert_equal(str, @obj.format('general'))
      assert_equal(str, @obj.general)
    end

    def test_format_endnote
      str = "%0 Journal Article\n%A Hoge, J.P.\n%A Fuga, F.B.\n%D 2001\n%T Title of the study.\n%J Theor. J. Hoge\n%V 12\n%N 3\n%P 123-145\n%M 12345678\n%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12345678\n%X Hoge fuga. hoge fuga.\n%K Hoge\n%+ Tokyo"
      assert_equal(str, @obj.format('endnote'))
      assert_equal(str, @obj.endnote)
    end

    def test_format_bibitem
      str = "\\bibitem{PMID:12345678}\nHoge, J.P., Fuga, F.B.\nTitle of the study.,\n{\\em Theor. J. Hoge}, 12(3):123--145, 2001."
      assert_equal(str, @obj.format('bibitem'))
      assert_equal(str, @obj.bibitem)
    end

    def test_format_bibtex
      str =<<END
        @article{PMID:12345678,
          author  = {Hoge, J.P. and Fuga, F.B.},
          title   = {Title of the study.},
          journal = {Theor. J. Hoge},
          year    = {2001},
          volume  = {12},
          number  = {3},
          pages   = {123--145},
        }
END
      assert_equal(str, @obj.format('bibtex'))
      assert_equal(str, @obj.bibtex)
    end

    def test_format_rd
      str = "== Title of the study.\n\n* Hoge, J.P. and Fuga, F.B.\n\n* Theor. J. Hoge 2001 12:123-145 [PMID:12345678]\n\nHoge fuga. hoge fuga."
      assert_equal(str, @obj.format('rd'))
      assert_equal(str, @obj.rd)
    end

    def test_format_nature
      str = 'Hoge, J.P. & Fuga, F.B. Title of the study. Theor. J. Hoge 12, 123-145 (2001).'
      assert_equal(str, @obj.format('Nature'))
      assert_equal(str, @obj.format('nature'))
      assert_equal(str, @obj.nature)
    end

    def test_format_science
      str = 'J.P. Hoge, F.B. Fuga, Theor. J. Hoge 12 123 (2001).'
      assert_equal(str, @obj.format('Science'))
      assert_equal(str, @obj.format('science'))
      assert_equal(str, @obj.science)
    end

    def test_format_genome_biol
      str = 'Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.'
      assert_equal(str, @obj.format('genome biol'))
      assert_equal(str, @obj.genome_biol)
    end

    def test_format_genome_res
      str = "Hoge, J.P. and Fuga, F.B. 2001.\n  Title of the study. Theor. J. Hoge 12: 123-145."
      assert_equal(str, @obj.format('genome res'))
      assert_equal(str, @obj.genome_res)
    end

    def test_format_nar
      str = 'Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge, 12, 123-145.'
      assert_equal(str, @obj.format('nar'))
      assert_equal(str, @obj.nar)
    end

    def test_format_current
      str = 'Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.'
      assert_equal(str, @obj.format('current biology'))
    end

    def test_format_trends
      str = 'Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge 12, 123-145'
      assert_equal(str, @obj.trends)
    end

    def test_format_cell
      str = 'Hoge, J.P. and Fuga, F.B. (2001). Title of the study. Theor. J. Hoge 12, 123-145.'
      assert_equal(str, @obj.format('cell'))
    end

  end

  class TestReferences < Test::Unit::TestCase

    def setup
      hash = {}
      ary = [Bio::Reference.new(hash),
             Bio::Reference.new(hash)]
      @obj = Bio::References.new(ary)
    end

    def test_append
      hash = {}
      ref = Bio::Reference.new(hash)
      assert(@obj.append(ref))
    end

    def test_each
      @obj.each do |ref|
        assert(ref)
      end
    end

  end

end