bio 1.2.1 → 1.3.0

data/test/unit/bio/io/test_ddbjxml.rb

@@ -4,7 +4,7 @@
 # Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::   The Ruby License
 #
-#  $Id: test_ddbjxml.rb,v 1.4 2007/04/05 23:35:43 trevor Exp $ 
+#  $Id:$ 
 #
 
 require 'pathname'
@@ -21,8 +21,9 @@ class TestDDBJXMLConstants < Test::Unit::TestCase
 
   def test_constants
     constants = ["DDBJ", "TxSearch", "ClustalW", "PML", "Gib", "Fasta", 
-                 "BASE_URI", "SRS", "SERVER_URI", "Gtop", "GetEntry", "Blast"].sort
-    assert_equal(constants, Bio::DDBJ::XML.constants.sort)
+                 "BASE_URI", "SRS", "SERVER_URI", "Gtop", "GetEntry",
+                 "Blast", "RequestManager"].sort
+    assert_equal(constants, Bio::DDBJ::XML.constants.sort.collect{|x| x.to_s})
   end
 
   def test_base_url
@@ -69,6 +70,10 @@ class TestDDBJXMLConstants < Test::Unit::TestCase
     assert_equal("http://xml.nig.ac.jp/wsdl/TxSearch.wsdl", Bio::DDBJ::XML::TxSearch::SERVER_URI)
   end
 
+  def test_requestmanager_server_url
+    assert_equal("http://xml.nig.ac.jp/wsdl/RequestManager.wsdl", Bio::DDBJ::XML::RequestManager::SERVER_URI)
+  end
+
 end
 
 

data/test/unit/bio/io/test_fastacmd.rb

@@ -4,7 +4,7 @@
 # Copyright::  Copyright (C) 2006 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_fastacmd.rb,v 1.3 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -20,11 +20,11 @@ module Bio
 class TestFastacmd < Test::Unit::TestCase
 
   def setup
-    @obj = Bio::Blast::Fastacmd.new("/tmp/test")
+    @obj = Bio::Blast::Fastacmd.new('/dev/null')
   end
 
   def test_database
-    assert_equal("/tmp/test", @obj.database)
+    assert_equal('/dev/null', @obj.database)
   end
 
   def test_fastacmd
@@ -32,9 +32,9 @@ class TestFastacmd < Test::Unit::TestCase
   end
 
   def test_methods
-    method_list = ['get_by_id', 'fetch', 'each_entry', 'each']
+    method_list = [ :get_by_id, :fetch, :each_entry, :each ]
     method_list.each do |method|
-      assert(@obj.methods.include?(method))
+      assert(@obj.respond_to?(method))
     end
   end
 

data/test/unit/bio/io/test_flatfile.rb

@@ -9,7 +9,7 @@
 #
 
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
 $:.unshift(libpath) unless $:.include?(libpath)
 
 require 'test/unit'
@@ -23,159 +23,410 @@ module TestFlatFile
 
   bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
   TestDataPath = Pathname.new(File.join(bioruby_root, 'test', 'data')).cleanpath.to_s
-  TestDataFastaFormat01 = File.join(TestDataPath, 'fasta', 'example1.txt')
+  TestData01 = File.join(TestDataPath, 'fasta', 'example1.txt')
+
+  TestData01Ent1def =
+    "At1g02580 mRNA (2291 bp) UTR's and CDS"
+  TestData01Ent4def =
+    'At1g65300: mRNA 837bp (shortened from start)'
+  TestData01Ent4naseq = Bio::Sequence::NA.new <<__END_OF_SEQ__
+ttcatctttacctcttcctattgttgcgaatgcagctgcaccagtcg
+gatttgatggtcctatgtttcaatatcataatcaaaatcagcaaaagccggttcaattccaatatcaggctcttta
+tgatttttatgatcagattccaaagaaaattcatggttttaatatgaatatgaataaggattcgaatcaaagtatg
+gttttggatttgaatcaaaatcttaatgatggagaggacgagggcattccttgcatggacaacaacaactaccacc
+ccgaaatcgattgtctcgctaccgtcaccactgcccccactgatgtttgtgctcctaacatcaccaatgatctcta
+g
+__END_OF_SEQ__
+
+  # test Bio::FlatFile class method
+  class TestFlatFileClassMethod < Test::Unit::TestCase
 
-  class TestBufferedInputStreamClassMethod < Test::Unit::TestCase
-    def test_self_for_io
-      io = File.open(TestDataFastaFormat01)
-      obj = Bio::FlatFile::BufferedInputStream.for_io(io)
-      assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
-      assert_equal(TestDataFastaFormat01, obj.path)
+    def setup
+      @filename = TestData01
+      @klass = Bio::FastaFormat
+    end
+
+    # test template for Bio::FlatFile.open
+    def open_TestData01(*arg)
+      assert_instance_of(Bio::FlatFile,
+                         ff = Bio::FlatFile.open(*arg))
+      assert_equal(@klass, ff.dbclass)
+      assert_nil(ff.close)
+    end
+    private :open_TestData01
+
+    # test template for Bio::FlatFile.open with block
+    def open_with_block_TestData01(*arg)
+      ret = Bio::FlatFile.open(*arg) do |ff|
+        assert_instance_of(Bio::FlatFile, ff)
+        assert_equal(@klass, ff.dbclass)
+        ff.each do |e|
+          assert_instance_of(@klass, e)
+          assert_instance_of(String, ff.entry_raw)
+        end
+        'test return value'
+      end
+      assert_equal('test return value', ret)
+    end
+    private :open_with_block_TestData01
+
+    def test_open_0arg
+      assert_raise(ArgumentError) { Bio::FlatFile.open }
+    end
+
+    def test_open_1arg_nil
+      assert_raise(ArgumentError) { Bio::FlatFile.open(nil) }
+    end
+
+    def test_open_1arg_class
+      assert_raise(ArgumentError) { Bio::FlatFile.open(Bio::GenBank) }
+    end
+
+    def test_open_1arg_filename
+      open_TestData01(@filename)
+    end
+
+    def test_open_1arg_io
+      io = File.open(@filename)
+      open_TestData01(io)
+      assert(io.closed?)
+    end
+
+    def test_open_1arg_with_block
+      open_with_block_TestData01(@filename)
+    end
+
+    def test_open_1arg_io_with_block
+      io = File.open(@filename)
+      open_with_block_TestData01(io)
+      # When IO object is given, the IO is NOT automatically closed.
+      assert_equal(false, io.closed?)
+      assert_nothing_raised { io.close }
+    end
+
+    def test_open_2arg_autodetect
+      open_TestData01(nil, @filename)
+    end
+
+    def test_open_2arg_autodetect_with_block
+      open_with_block_TestData01(nil, @filename)
+    end
+
+    def test_open_2arg_autodetect_io
+      io = File.open(@filename)
+      open_TestData01(nil, io)
+      assert(io.closed?)
+    end
+
+    def test_open_2arg_autodetect_io_with_block
+      io = File.open(@filename)
+      open_with_block_TestData01(nil, io)
+      # When IO object is given, the IO is NOT automatically closed.
+      assert_equal(false, io.closed?)
+      assert_nothing_raised { io.close }
+    end
+
+    def test_open_2arg_class
+      open_TestData01(@klass, @filename)
+    end
+
+    def test_open_2arg_class_with_block
+      open_with_block_TestData01(@klass, @filename)
+    end
+
+    def test_open_2arg_class_io
+      io = File.open(@filename)
+      open_TestData01(@klass, io)
+      assert(io.closed?)
+    end
+
+    def test_open_2arg_class_io_with_block
+      io = File.open(@filename)
+      open_with_block_TestData01(@klass, io)
+      # When IO object is given, the IO is NOT automatically closed.
+      assert_equal(false, io.closed?)
+      assert_nothing_raised { io.close }
+    end
+
+    def test_open_2arg_filename_mode
+      open_TestData01(@filename, 'r')
+    end
+
+    def test_open_2arg_filename_mode_with_block
+      open_with_block_TestData01(@filename, 'r')
+    end
+
+    def test_open_3arg
+      open_TestData01(nil, @filename, 'r')
+      open_TestData01(@klass, @filename, 'r')
+      open_TestData01(@filename, File::RDONLY, 0)
+    end
+
+    def test_open_3arg_with_block
+      open_with_block_TestData01(nil, @filename, 'r')
+      open_with_block_TestData01(@klass, @filename, 'r')
+      open_with_block_TestData01(@filename, File::RDONLY, 0)
     end
 
-    def test_self_open_file
-      obj = Bio::FlatFile::BufferedInputStream.open_file(TestDataFastaFormat01)
-      assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
-      assert_equal(TestDataFastaFormat01, obj.path)
+    def test_open_4arg
+      open_TestData01(nil, @filename, File::RDONLY, 0)
+      open_TestData01(Bio::FastaFormat,
+                                 @filename, File::RDONLY, 0)
+
+      open_with_block_TestData01(nil, @filename, File::RDONLY, 0)
+      open_with_block_TestData01(Bio::FastaFormat,
+                                            @filename, File::RDONLY, 0)
+    end
+
+    # test template for Bio::FlatFile.auto
+    def auto_TestData01(*arg)
+      assert_instance_of(Bio::FlatFile,
+                         ff = Bio::FlatFile.auto(*arg))
+      assert_equal(@klass, ff.dbclass)
+      assert_nil(ff.close)
+    end
+    private :auto_TestData01
+
+    # test template for Bio::FlatFile.auto with block
+    def auto_with_block_TestData01(*arg)
+      ret = Bio::FlatFile.auto(*arg) do |ff|
+        assert_instance_of(Bio::FlatFile, ff)
+        assert_equal(@klass, ff.dbclass)
+        ff.each do |e|
+          assert_instance_of(@klass, e)
+          assert_instance_of(String, ff.entry_raw)
+        end
+        'test return value'
+      end
+      assert_equal('test return value', ret)
+    end
+    private :auto_with_block_TestData01
+
+    def test_auto_0arg
+      assert_raise(ArgumentError) { Bio::FlatFile.auto }
+    end
+
+    def test_auto_1arg_filename
+      auto_TestData01(@filename)
+    end
+
+    def test_auto_1arg_io
+      io = File.open(@filename)
+      auto_TestData01(io)
+      assert(io.closed?)
+    end
+
+    def test_auto_1arg_with_block
+      auto_with_block_TestData01(@filename)
+    end
+
+    def test_auto_1arg_io_with_block
+      io = File.open(@filename)
+      auto_with_block_TestData01(io)
+      # When IO object is given, the IO is NOT automatically closed.
+      assert_equal(false, io.closed?)
+      assert_nothing_raised { io.close }
+    end
+
+    def test_auto_2arg_filename_mode
+      auto_TestData01(@filename, 'r')
+    end
+
+    def test_auto_2arg_filename_mode_with_block
+      auto_with_block_TestData01(@filename, 'r')
+    end
+
+    def test_auto_3arg
+      auto_TestData01(@filename, File::RDONLY, 0)
     end
 
-    def test_self_open_file_with_block
-      obj2 = nil
-      Bio::FlatFile::BufferedInputStream.open_file(TestDataFastaFormat01) do |obj|
-        assert_instance_of(Bio::FlatFile::BufferedInputStream, obj)
-        assert_equal(TestDataFastaFormat01, obj.path)
-        obj2 = obj
+    def test_auto_3arg_with_block
+      auto_with_block_TestData01(@filename, File::RDONLY, 0)
+    end
+
+    def test_to_a
+      assert_instance_of(Array,
+                         a = Bio::FlatFile.to_a(@filename))
+      assert_equal(5, a.size)
+      assert_instance_of(Bio::FastaFormat, a[3])
+      assert_equal(TestData01Ent4def,
+                   a[3].definition)
+
+      assert_equal(TestData01Ent4naseq, a[3].naseq)
+    end
+
+    def test_foreach
+      Bio::FlatFile.foreach(@filename) do |ent|
+        assert_instance_of(Bio::FastaFormat, ent)
       end
-      assert_raise(IOError) { obj2.close }
     end
-  end #class TestBufferedInputStreamClassMethod
 
-  class TestBufferedInputStream < Test::Unit::TestCase
+    def test_new_2arg_nil
+      io = File.open(@filename)
+      assert_instance_of(Bio::FlatFile,
+                         ff = Bio::FlatFile.new(nil, io))
+      assert_equal(@klass, ff.dbclass)
+      assert_nil(ff.close)
+    end
+
+    def test_new_2arg_class
+      io = File.open(@filename)
+      assert_instance_of(Bio::FlatFile,
+                         ff = Bio::FlatFile.new(@klass, io))
+      assert_equal(@klass, ff.dbclass)
+      assert_nil(ff.close)
+    end
+
+  end #class TestFlatFileClassMethod
+
+  # test Bio::FlatFile instance methods
+  class TestFlatFileFastaFormat < Test::Unit::TestCase
     def setup
-      io = File.open(TestDataFastaFormat01)
-      path = TestDataFastaFormat01
-      @obj = Bio::FlatFile::BufferedInputStream.new(io, path)
+      @klass = Bio::FastaFormat
+      @filename = TestData01
+      @ff = Bio::FlatFile.open(@klass, @filename)
     end
 
     def test_to_io
-      assert_kind_of(IO, @obj.to_io)
+      assert_instance_of(File, @ff.to_io)
     end
 
-    def test_close
-      assert_nil(@obj.close)
+    def test_path
+      assert_equal(@filename, @ff.path)
     end
 
-    def test_rewind
-      @obj.prefetch_gets
-      @obj.rewind
-      assert_equal('', @obj.prefetch_buffer)
+    def test_next_entry
+      assert_instance_of(@klass, ent = @ff.next_entry)
+      assert_equal(TestData01Ent1def, ent.definition)
+      assert_instance_of(@klass, ent = @ff.next_entry)
+      assert_instance_of(@klass, ent = @ff.next_entry)
+      assert_instance_of(@klass, ent = @ff.next_entry)
+      assert_equal(TestData01Ent4def, ent.definition)
+      assert_equal(TestData01Ent4naseq, ent.naseq)
     end
 
-    def test_pos
-      @obj.gets
-      @obj.gets
-      @obj.prefetch_gets
-      assert_equal(117, @obj.pos) #the number depends on original data
+    def test_entry_raw
+      4.times { @ff.next_entry }
+      assert_instance_of(String, str = @ff.entry_raw)
+      assert_equal(TestData01Ent4def, @klass.new(str).definition)
+      assert_equal(TestData01Ent4naseq, @klass.new(str).naseq)
     end
 
-    def test_pos=()
-      str = @obj.gets
-      assert_equal(0, @obj.pos = 0)
+    def test_entry_pos_flag
+      # default is nil
+      assert_equal(nil, @ff.entry_pos_flag)
+      # set as true
+      assert_equal(true, @ff.entry_pos_flag = true)
+      assert_equal(true, @ff.entry_pos_flag)
     end
-      
-    def test_eof_false_first
-      assert_equal(false, @obj.eof?)
+
+    def test_start_pos_ended_pos_not_recorded
+      # default is nil
+      assert_equal(nil, @ff.entry_start_pos)
+      #
+      @ff.entry_pos_flag = false
+      @ff.next_entry
+      # nil if not recorded
+      assert_equal(nil, @ff.entry_start_pos)
+      assert_equal(nil, @ff.entry_ended_pos)
+      @ff.next_entry
+      # nil if not recorded
+      assert_equal(nil, @ff.entry_start_pos)
+      assert_equal(nil, @ff.entry_ended_pos)
     end
 
-    def test_eof_false_after_prefetch
-      while @obj.prefetch_gets; nil; end
-      assert_equal(false, @obj.eof?)
+    def test_start_pos
+      @ff.entry_pos_flag = true
+      @ff.next_entry
+      assert_equal(0, @ff.entry_start_pos)
+      @ff.next_entry
+      # On Windows, the values might be different.
+      assert_equal(2367, @ff.entry_start_pos)
     end
 
-    def test_eof_true
-      while @obj.gets; nil; end
-      assert_equal(true, @obj.eof?)
+    def test_ended_pos
+      @ff.entry_pos_flag = true
+      @ff.next_entry
+      # On Windows, the values might be different.
+      assert_equal(2367, @ff.entry_ended_pos)
+      @ff.next_entry
+      # On Windows, the values might be different.
+      assert_equal(3244, @ff.entry_ended_pos)
     end
 
-    def test_gets
-      @obj.gets
-      @obj.gets
-      assert_equal("gagcaaatcgaaaaggagagatttctgcatatcaagagaaaattcgagctgagatacattccaagtgtggctactc", @obj.gets.chomp)
+    def test_each_entry
+      i = 0
+      @ff.each_entry do |ent|
+        assert_instance_of(@klass, ent)
+        i += 1
+        if i == 4 then
+          assert_equal(TestData01Ent4def, ent.definition)
+          assert_equal(TestData01Ent4naseq, ent.naseq)
+        end
+      end
     end
 
-    def test_gets_equal_prefetch_gets
-      @obj.prefetch_gets
-      str = @obj.prefetch_gets
-      @obj.prefetch_gets
-      @obj.gets
-      assert_equal(@obj.gets, str)
+    # each is an alias of each_entry
+    def test_each
+      assert_nothing_raised { @ff.each {} }
     end
 
-    def test_ungets
-      @obj.gets
-      @obj.gets
-      str1 = @obj.gets
-      str2 = @obj.gets
-      assert_nil(@obj.ungets(str2))
-      assert_nil(@obj.ungets(str1))
-      assert_equal(str1, @obj.gets)
-      assert_equal(str2, @obj.gets)
+    def test_rewind
+      @ff.next_entry
+      assert_not_equal(0, @ff.pos)
+      assert_equal(0, @ff.rewind)
+      assert_equal(0, @ff.pos)
     end
 
-    def test_getc
-      assert_equal(?>, @obj.getc)
+    def test_close
+      assert_nil(@ff.close)
     end
 
-    def test_getc_after_prefetch
-      @obj.prefetch_gets
-      assert_equal(?>, @obj.getc)
+    def test_pos
+      assert_equal(0, @ff.pos)
+      @ff.next_entry
+      assert_not_equal(0, @ff.pos)
     end
 
-    def test_ungetc
-      c = @obj.getc
-      assert_nil(@obj.ungetc(c))
-      assert_equal(c, @obj.getc)
+    def test_eof?
+      5.times { @ff.next_entry }
+      assert_equal(true, @ff.eof?)
     end
 
-    def test_ungetc_after_prefetch
-      str = @obj.prefetch_gets
-      c = @obj.getc
-      assert_nil(@obj.ungetc(c))
-      assert_equal(str, @obj.gets)
+    def test_raw
+      # default false
+      assert_equal(false, @ff.raw)
+      # changes to true
+      assert_equal(true, @ff.raw = true)
+      @ff.each do |ent|
+        assert_instance_of(String, ent)
+      end
     end
 
-    def test_prefetch_buffer
-      str = @obj.prefetch_gets
-      str += @obj.prefetch_gets
-      assert_equal(str, @obj.prefetch_buffer)
+    def test_dbclass
+      assert_equal(@klass, @ff.dbclass)
     end
 
-    def test_prefetch_gets
-      @obj.prefetch_gets
-      @obj.prefetch_gets
-      @obj.gets
-      str = @obj.prefetch_gets
-      @obj.gets
-      assert_equal(str, @obj.gets)
+    def test_dbclass_eq
+      klass = Bio::FastaNumericFormat
+      assert_equal(klass, @ff.dbclass = klass)
+      assert_equal(klass, @ff.dbclass)
     end
 
-    def test_prefetch_gets_with_arg
-      # test @obj.gets
-      str = @obj.prefetch_gets("\n>")
-      assert_equal(str, @obj.gets("\n>"))
-      # test using IO object
-      io = @obj.to_io
-      io.rewind
-      assert_equal(str, io.gets("\n>"))
+    def test_dbclass_nil
+      assert_equal(nil, @ff.dbclass = nil)
+      assert_equal(nil, @ff.dbclass)
+      assert_raise(Bio::FlatFile::UnknownDataFormatError) { @ff.next_entry }
     end
 
-    def test_skip_spaces
-      @obj.gets('CDS')
-      assert_nil(@obj.skip_spaces)
-      assert_equal(?a, @obj.getc)
+    def test_autodetect
+      @ff.dbclass = nil
+      assert_equal(@klass, @ff.autodetect)
+      assert_equal(@klass, @ff.dbclass)
     end
-                   
-  end #class TestBufferedInputStream
+
+  end #class TestFlatFileFastaFormat
+
 
   class TestFlatFileWithCustomClass < Test::Unit::TestCase