bio 1.4.2 → 1.4.3

data/test/bioruby_test_helper.rb

@@ -14,26 +14,51 @@ unless defined? BioRubyTestDebug then
   end
 end #BioRubyTestDebug
 
-unless defined? BioRubyTestLibPath and BioRubyTestLibPath then
+unless defined? BioRubyTestGem then
+  gem_version = ENV['BIORUBY_TEST_GEM']
+  if gem_version then
+    $stderr.puts 'require "rubygems"' if BioRubyTestDebug
+    require "rubygems"
+    if gem_version.empty? then
+      $stderr.puts "gem 'bio'" if BioRubyTestDebug
+      gem 'bio'
+    else
+      $stderr.puts "gem 'bio', #{gem_version.inspect}" if BioRubyTestDebug
+      gem 'bio', gem_version
+    end
+  end
+  BioRubyTestGem = gem_version
+end
+
+unless defined? BioRubyTestLibPath then
   libpath = ENV['BIORUBY_TEST_LIB']
-  if libpath.to_s.empty? then
+  unless libpath then
     libpath = Pathname.new(File.join(File.dirname(__FILE__),
                                      "..", "lib")).cleanpath.to_s
   end
-  libpath.freeze
 
-  unless $:.include?(libpath)
-    $:.unshift(libpath)
-    if BioRubyTestDebug then
-      $stderr.puts "Added #{libpath.inspect} to $:."
-    end
-  else
-    if BioRubyTestDebug then
-      $stderr.puts "NOT added #{libpath.inspect} to $:. because it is already in $:."
+  # do not add path to $: if BIORUBY_TEST_LIB is empty string
+  # or BioRubyTestGem is true.
+  if (libpath and libpath.empty?) or BioRubyTestGem then
+    libpath = nil
+  end
+
+  if libpath then
+    libpath.freeze
+
+    unless $:[0] == libpath then
+      $:.unshift(libpath)
+      if BioRubyTestDebug then
+        $stderr.puts "Added #{libpath.inspect} to $:."
+      end
+    else
+      if BioRubyTestDebug then
+        $stderr.puts "NOT added #{libpath.inspect} to $:. because it is already on the top of $:."
+      end
     end
   end
 
-  # (String) Path to be added to $:.
+  # (String or nil) Path to be added to $:.
   # It may or may not be the path of bioruby.
   BioRubyTestLibPath = libpath
   

data/test/data/KEGG/test.kgml

@@ -0,0 +1,37 @@
+<?xml version="1.0"?>
+<!DOCTYPE pathway SYSTEM "http://www.genome.jp/kegg/xml/KGML_v0.7.1_.dtd">
+<!-- mock data for testing lower-level parser functionality -->
+<pathway name="path:xxx09876" org="xxx" number="09876"
+         title="This is test title"
+         image="http://example.com/pathway/ec/09876.png"
+         link="http://example.com/show_pathway?xxx09876">
+    <entry id="1234" name="cpd:C99999" type="compound"
+        link="http://example.com/dbget-bin/www_bget?C99999">
+        <graphics name="C99999" fgcolor="#E0E0E0" bgcolor="#D0E0F0"
+             type="circle" x="1314" y="1008" width="14" height="28"/>
+    </entry>
+    <entry id="1" name="ec:1.1.1.1" type="enzyme" reaction="rn:R99999"
+        link="http://example.com/dbget-bin/www_bget?1.1.1.1">
+        <graphics name="1.1.1.1" fgcolor="#99CCFF" bgcolor="#FFFFFF"
+             type="line" coords="314,159,265,358,979,323"/>
+        <graphics name="1.1.1.1" fgcolor="#FF99CC" bgcolor="#CC99FF"
+             type="line" coords="271,828,182,845"/>
+    </entry>
+    <entry id="567" name="undefined" type="group">
+        <graphics fgcolor="#000000" bgcolor="#FFFFFF"
+             type="rectangle" x="1242" y="1134" width="456" height="678"/>
+        <component id="34"/>
+        <component id="56"/>
+        <component id="78"/>
+        <component id="90"/>
+    </entry>
+    <relation entry1="109" entry2="87" type="ECrel">
+        <subtype name="compound" value="100"/>
+    </relation>
+    <reaction id="3" name="rn:R99999 rn:R99998" type="reversible">
+        <substrate id="3330" name="cpd:C99990"/>
+        <substrate id="3331" name="cpd:C99991"/>
+        <product id="3332" name="cpd:C99902"/>
+        <product id="3333" name="cpd:C99903"/>
+    </reaction>
+</pathway>

data/test/data/command/echoarg2.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+/bin/echo "$2"
+

data/test/functional/bio/test_command.rb

@@ -19,22 +19,26 @@ require 'tempfile'
 require 'bio/command'
 
 module Bio
-  class FuncTestCommandCall < Test::Unit::TestCase
+  module FuncTestCommandCallCommon
 
-    def setup
-      if Bio::Command.module_eval { windows_platform? } then
-        cmd = File.expand_path(File.join(BioRubyTestDataPath, 'command', 'echoarg2.bat'))
-        @arg = [ cmd, 'test "argument 1"', '"test" argument 2', 'arg3' ]
-        @expected = '"""test"" argument 2"'
+    def windows_platform?
+      Bio::Command.module_eval { windows_platform? }
+    end
+    module_function :windows_platform?
+
+    def setup_cmd
+      if windows_platform? then
+        [ File.expand_path(File.join(BioRubyTestDataPath, 'command', 'echoarg2.bat')) ]
       else
-        cmd = "/bin/echo"
-        @arg = [ cmd, "test (echo) command" ]
-        @expected = "test (echo) command"
-        unless FileTest.executable?(cmd) then
-          raise "Unsupported environment: /bin/echo not found"
+        [ "/bin/sh", "/bin/echo" ].each do |cmd|
+          unless FileTest.executable?(cmd) then
+            raise "Unsupported environment: #{cmd} not found"
+          end
         end
+        [ "/bin/sh", File.expand_path(File.join(BioRubyTestDataPath, 'command', 'echoarg2.sh')) ]
       end
     end
+    private :setup_cmd
 
     def test_call_command
       ret = Bio::Command.call_command(@arg) do |io|
@@ -85,7 +89,49 @@ module Bio
       assert_equal(@expected, ret.to_s.strip)
     end
 
-  end #class FuncTestCommandCall
+  end #module FuncTestCommandCallCommon
+
+  class FuncTestCommandCallSimple < Test::Unit::TestCase
+
+    include FuncTestCommandCallCommon
+
+    def setup
+      @arg = setup_cmd
+      @arg.concat [ "first", "second", "third" ]
+      @expected = "second"
+    end
+  end #class FuncTestCommandCallSimple
+
+  class FuncTestCommandCallWithSpace < Test::Unit::TestCase
+
+    include FuncTestCommandCallCommon
+
+    def setup
+      @arg = setup_cmd
+      @arg.concat [ "this is", "a test for", "escape of space" ]
+      if windows_platform? then
+        @expected = '"a test for"'
+      else
+        @expected = "a test for"
+      end
+    end
+  end #class FuncTestCommandCallWithSpace
+
+  class FuncTestCommandCallMisc1 < Test::Unit::TestCase
+
+    include FuncTestCommandCallCommon
+
+    def setup
+      @arg = setup_cmd
+      @arg.concat [ 'test (a) *.* \'argument 1\'',
+                    '\'test\' (b) *.* argument 2', 'arg3' ]
+      if windows_platform? then
+        @expected = '"\'test\' (b) *.* argument 2"'
+      else
+        @expected = '\'test\' (b) *.* argument 2'
+      end
+    end
+  end #class FuncTestCommandCallMisc1
 
   class FuncTestCommandQuery < Test::Unit::TestCase
 
@@ -332,20 +378,4 @@ module Bio
     end
   end #class FuncTestCommandTmpdir
 
-  class FuncTestCommandNet < Test::Unit::TestCase
-    def test_read_uri
-      assert_nothing_raised {
-        Bio::Command.read_uri("http://bioruby.open-bio.org/")
-      }
-    end
-
-    def test_start_http
-    end
-
-    def test_new_http
-    end
-
-    def test_post_form
-    end
-  end #class FuncTestCommandNet
 end #module Bio

data/test/network/bio/test_command.rb

@@ -0,0 +1,35 @@
+#
+# test/network/bio/test_command.rb - Functional test for network connection methods in Bio::Command
+#
+# Copyright::	Copyright (C) 2008, 2011
+# 		Naohisa Goto <ng@bioruby.org>
+# License::	The Ruby License
+#
+
+# 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/command'
+
+module Bio
+  class FuncTestCommandNet < Test::Unit::TestCase
+    def test_read_uri
+      assert_nothing_raised {
+        Bio::Command.read_uri("http://bioruby.open-bio.org/")
+      }
+    end
+
+    def test_start_http
+    end
+
+    def test_new_http
+    end
+
+    def test_post_form
+    end
+  end #class FuncTestCommandNet
+end

data/test/runner.rb

@@ -8,25 +8,35 @@ load Pathname.new(File.join(File.dirname(__FILE__),
 # libraries needed for the tests
 require 'test/unit'
 
+unit_test = File.join(File.dirname($0), "unit")
+func_test = File.join(File.dirname($0), "functional")
+
 if !defined?(Test::Unit::AutoRunner) then
   # Ruby 1.9.1 does not have Test::Unit::AutoRunner
   Test::Unit.setup_argv do |files|
-    [ File.dirname($0) ]
+    [ unit_test, func_test ]
   end
   # tests called when exiting the program
 
 elsif defined?(Test::Unit::Color) then
   # workaround for test-unit-2.0.x
   r = Test::Unit::AutoRunner.new(true)
-  r.to_run.push File.dirname($0)
+  r.to_run.push unit_test
+  r.to_run.push func_test
+  r.process_args(ARGV)
+  exit r.run
+
+elsif RUBY_VERSION > "1.8.2" then
+  r = Test::Unit::AutoRunner.new(true) do |ar|
+    ar.to_run.push unit_test
+    ar.to_run.push func_test
+    [ unit_test, func_test ]
+  end
   r.process_args(ARGV)
   exit r.run
 
-elsif RUBY_VERSION > "1.8.2"
-  # current Test::Unit -- Ruby 1.8.3 or later
-  exit Test::Unit::AutoRunner.run(true, File.dirname($0))
 else
   # old Test::Unit -- Ruby 1.8.2 or older
-  exit Test::Unit::AutoRunner.run(false, File.dirname($0))
+  raise "Ruby version too old. Please use newer version of Ruby."
 end
 

data/test/unit/bio/appl/blast/test_report.rb

@@ -614,6 +614,125 @@ module Bio
     end
   end
 
+  module TestBlastReportTabularHelper
+    def def_test_assert_nil(test_method)
+      str = test_method.to_s
+      name = str.sub(/test(\_(Hit|Hsp))?\_/, '')
+      method = name.intern
+      instance = case self.to_s
+                 when /Iteration/
+                   :@itr
+                 when /Hit/
+                   :@hit
+                 when /Hsp/
+                   :@hsp
+                 else
+                   :@report
+                 end
+                  
+      define_method(test_method) do
+        assert_nil(instance_variable_get(instance).__send__(method))
+      end
+    end
+  end #module 
+
+  class TestBlastReportTabular < TestBlastReport
+    extend TestBlastReportTabularHelper
+
+    def_test_assert_nil :test_db
+    def_test_assert_nil :test_db_len
+    def_test_assert_nil :test_db_num
+    def_test_assert_nil :test_eff_space
+    def_test_assert_nil :test_entropy
+    def_test_assert_nil :test_expect
+    def_test_assert_nil :test_filter
+    def_test_assert_nil :test_gap_extend
+    def_test_assert_nil :test_gap_open
+    def_test_assert_nil :test_hsp_len
+    def_test_assert_nil :test_kappa
+    def_test_assert_nil :test_lambda
+    def_test_assert_nil :test_matrix
+    def_test_assert_nil :test_program
+    def_test_assert_nil :test_query_len
+    def_test_assert_nil :test_reference
+    def_test_assert_nil :test_version
+
+    # No parameters information available in the "-m 8" format
+    def test_parameters
+      assert_equal({}, @report.parameters)
+    end
+
+    def test_query_def
+      # differs from XML because of truncation in the "-m 8" format
+      assert_equal("eco:b0002", @report.query_def)
+    end
+
+    def test_query_id
+      # differs from XML because of the limited data
+      assert_equal("eco:b0002", @report.query_id)
+    end
+
+    # No statistics information available in the "-m 8" format
+    def test_statistics
+      assert_equal({}, @report.statistics)
+    end
+  end #class TestBlastReportTabular
+
+  class TestBlastReportIterationTabular < TestBlastReportIteration
+
+    # No statistics information available in the "-m 8" format
+    def test_statistics
+      assert_equal({}, @itr.statistics)
+    end
+  end #class TestBlastReportIterationTabular
+
+  class TestBlastReportHitTabular < TestBlastReportHit
+    extend TestBlastReportTabularHelper
+
+    def_test_assert_nil :test_Hit_hit_id
+    def_test_assert_nil :test_Hit_identity
+    def_test_assert_nil :test_Hit_len
+    def_test_assert_nil :test_Hit_midline
+    def_test_assert_nil :test_Hit_query_len
+    def_test_assert_nil :test_Hit_query_seq
+    def_test_assert_nil :test_Hit_target_len
+    def_test_assert_nil :test_Hit_target_seq
+
+    def test_Hit_bit_score
+      # differs from XML because of truncation in the "-m 8" format
+      assert_equal(1567.0, @hit.bit_score)
+    end
+
+    def test_Hit_query_def
+      # differs from XML because of truncation in the "-m 8" format
+      assert_equal("eco:b0002", @hit.query_def)
+    end
+
+    def test_Hit_query_id
+      # differs from XML because of the limited data
+      assert_equal("eco:b0002", @hit.query_id)
+    end
+  end #class TestBlastReportHitTabular
+
+  class TestBlastReportHspTabular < TestBlastReportHsp
+    extend TestBlastReportTabularHelper
+
+    def_test_assert_nil :test_Hsp_density
+    def_test_assert_nil :test_Hsp_hit_frame
+    def_test_assert_nil :test_Hsp_hseq
+    def_test_assert_nil :test_Hsp_identity
+    def_test_assert_nil :test_Hsp_midline
+    def_test_assert_nil :test_Hsp_positive
+    def_test_assert_nil :test_Hsp_qseq
+    def_test_assert_nil :test_Hsp_query_frame
+    def_test_assert_nil :test_Hsp_score
+
+    def test_Hsp_bit_score
+      # differs from XML because of truncation in the "-m 8" format
+      assert_equal(1567.0, @hsp.bit_score)
+    end
+  end #class TestBlastReportHspTabular
+
   ########################################################################
   # Tests for new BLAST XML format (blastall 2.2.14 or later)
   # with the result of multiple query sequences

data/test/unit/bio/appl/blast/test_rpsblast.rb

@@ -26,6 +26,7 @@ module TestRPSBlast
   class TestRPSBlastSplitter < Test::Unit::TestCase
     def setup
       @io = File.open(TestFileName)
+      @io.binmode
       @bstream = Bio::FlatFile::BufferedInputStream.new(@io, TestFileName)
       @klass = Bio::Blast::RPSBlast::Report
       @splitter = Bio::Blast::RPSBlast::RPSBlastSplitter.new(@klass, @bstream)