Newly added functional test for Bio::PubMed.

test/functional/bio/io/test_pubmed.rb

@@ -0,0 +1,129 @@
+#
+# test/functional/bio/io/test_pubmed.rb - Functional test for Bio::PubMed
+#
+# Copyright::   Copyright (C) 2009
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+#  $Id:$
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'bio/io/pubmed'
+require 'bio/db/medline'
+require 'test/unit'
+
+module Bio
+
+  module FuncTestPubmedCommon
+
+    def test_esearch
+      a = @pm.esearch('agile bioinformatics')
+      assert_kind_of(Array, a)
+      assert_operator(a.size, :>=, 3,
+                      'The failure may be caused by changes of NCBI PubMed.')
+      a.each do |x|
+        assert_kind_of(String, x)
+        assert_equal(x.strip, x.to_i.to_s,
+                     'PMID is not an integer value. This suggests that NCBI have changed the PMID policy.')
+      end
+    end
+
+    def test_esearch_count
+      a = @pm.esearch('agile bioinformatics',
+                      { "rettype"=>"count" })
+      assert_kind_of(Integer, a)
+      assert_operator(a, :>=, 3,
+                      'The failure may be caused by changes of NCBI PubMed.')
+    end
+
+    def test_esearch_retmax_retstart
+      a = @pm.esearch('p53', { "retmax" => 10, "retstart" => 20 })
+      assert_equal(10, a.size,
+                   'The failure may be caused by changes of NCBI PubMed.')
+      a.each do |x|
+        assert_kind_of(String, x)
+        assert_equal(x.strip, x.to_i.to_s,
+                     'PMID is not an integer value. This suggests that NCBI have changed the PMID policy.')
+      end
+
+      a1 = @pm.esearch('p53', { "retmax" => 15, "retstart" => 35 })
+      a2 = @pm.esearch('p53', { "retmax" => 10, "retstart" => 0 })
+      assert_equal(35, (a + a1 + a2).sort.uniq.size,
+                   'The failure may be caused by changes of NCBI PubMed.')
+
+      a3 = @pm.esearch('p53', { "retmax" => 10 })
+      assert_equal(a2.sort, a3.sort,
+                   'The failure may be caused by changes of NCBI PubMed.')
+    end
+
+    def check_pubmed_entry(pmid, str)
+      m = Bio::MEDLINE.new(str)
+      assert_equal(pmid.to_s, m.pmid)
+    end
+    private :check_pubmed_entry
+
+    def do_efetch_single(pmid)
+      a = @pm.efetch(pmid)
+      assert_kind_of(Array, a)
+      assert_equal(1, a.size)
+      check_pubmed_entry(pmid, a[0])
+    end
+    private :do_efetch_single
+
+    def test_efetch
+      do_efetch_single(12368254)
+    end
+
+    def test_efetch_str
+      do_efetch_single("16734914")
+    end
+
+    def test_efetch_multiple
+      arg = [ 12368254, 18689808, 19304878 ]
+      a = @pm.efetch(arg)
+      assert_kind_of(Array, a)
+      assert_equal(3, a.size)
+      a.each do |str|
+        check_pubmed_entry(arg.shift, str)
+      end
+    end
+
+    def test_efetch_single_xml
+      arg = 12368254
+      str = @pm.efetch(arg, { "retmode" => 'xml' })
+      assert_kind_of(String, str)
+      assert(str.index(/\<PubmedArticleSet\>/))
+    end
+
+    def test_efetch_multiple_xml
+      arg = [ "16734914", 16381885, "10592173" ]
+      str = @pm.efetch(arg, { "retmode" => 'xml' })
+      assert_kind_of(String, str)
+      assert(str.index(/\<PubmedArticleSet\>/))
+    end
+
+  end #module FuncTestPubmedCommon
+
+  class FuncTestPubmed < Test::Unit::TestCase
+
+    include FuncTestPubmedCommon
+
+    def setup
+      @pm = Bio::PubMed.new
+    end
+  end #class FuncTestPubmed
+
+  class FuncTestPubmedClassMethod < Test::Unit::TestCase
+
+    include FuncTestPubmedCommon
+
+    def setup
+      @pm = Bio::PubMed
+    end
+  end #class FuncTestPubmedClassMethod
+
+end