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#
# = test/unit/bio/test_reference.rb - Unit test for Bio::Reference
#
# Copyright:: Copyright (C) 2006
# Mitsuteru C. Nakao <n@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
# loading helper routine for testing bioruby
require 'pathname'
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
'bioruby_test_helper.rb')).cleanpath.to_s
# libraries needed for the tests
require 'test/unit'
require 'bio/reference'
require 'bio/compat/references'
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_pubmed_url
assert_equal("http://www.ncbi.nlm.nih.gov/pubmed/12345678",
@obj.pubmed_url)
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://example.com\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},
url = {http://example.com},
}
__END__
assert_equal(str, @obj.format('bibtex'))
assert_equal(str, @obj.bibtex)
end
def test_format_bibtex_with_arguments
str =<<__END__
@inproceedings{YourArticle,
author = {Hoge, J.P. and Fuga, F.B.},
title = {Title of the study.},
year = {2001},
volume = {12},
number = {3},
pages = {123--145},
booktitle = {Theor. J. Hoge},
month = {December},
}
__END__
assert_equal(str, @obj.format('bibtex', 'inproceedings', 'YourArticle',
{ 'journal' => false,
'url' => false,
'booktitle' => @obj.journal,
'month' => 'December'}))
assert_equal(str, @obj.bibtex('inproceedings', 'YourArticle',
{ 'journal' => false,
'url' => false,
'booktitle' => @obj.journal,
'month' => 'December'}))
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 TestReference_noURL < 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.",
'mesh' => ['Hoge'],
'affiliations' => ['Tokyo']
}
@obj = Bio::Reference.new(hash)
end
def test_url
assert_equal(nil, @obj.url)
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/pubmed/12345678\n%X Hoge fuga. hoge fuga.\n%K Hoge\n%+ Tokyo"
assert_equal(str, @obj.format('endnote'))
assert_equal(str, @obj.endnote)
end
end #class TestReference_noURL
class TestReferences < Test::Unit::TestCase
class NullStderr
def initialize
@log = []
end
def write(*arg)
#p arg
@log.push([ :write, *arg ])
nil
end
def method_missing(*arg)
#p arg
@log.push arg
nil
end
end #class NullStderr
def setup
# To suppress warning messages, $stderr is replaced by dummy object.
@stderr_orig = $stderr
$stderr = NullStderr.new
hash = {}
ary = [Bio::Reference.new(hash),
Bio::Reference.new(hash)]
@obj = Bio::References.new(ary)
end
def teardown
# bring back $stderr
$stderr = @stderr_orig
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
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