bio 1.3.1 → 1.4.0

data/test/functional/bio/appl/test_pts1.rb

@@ -8,10 +8,12 @@
 # $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/pts1'
 
@@ -76,9 +78,9 @@ END
     end
     
 
-    def test_output_size
-      assert_equal(1634, @report.output.size)
-    end
+    #def test_output_size
+    #  assert_equal(1634, @report.output.size)
+    #end
 
     def test_entry_id
       assert_equal("hoge", @report.entry_id)

data/test/functional/bio/io/test_ensembl.rb

@@ -8,11 +8,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
-
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/io/ensembl'
 

data/test/functional/bio/io/test_pubmed.rb

@@ -8,13 +8,15 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
+require 'test/unit'
 require 'bio/io/pubmed'
 require 'bio/db/medline'
-require 'test/unit'
 
 module Bio
 
@@ -113,6 +115,8 @@ module Bio
     include FuncTestPubmedCommon
 
     def setup
+      Bio::NCBI.default_email = 'staff@bioruby.org'
+      #$stderr.puts Bio::NCBI.default_tool
       @pm = Bio::PubMed.new
     end
   end #class FuncTestPubmed
@@ -122,6 +126,8 @@ module Bio
     include FuncTestPubmedCommon
 
     def setup
+      Bio::NCBI.default_email = 'staff@bioruby.org'
+      #$stderr.puts Bio::NCBI.default_tool
       @pm = Bio::PubMed
     end
   end #class FuncTestPubmedClassMethod

data/test/functional/bio/io/test_soapwsdl.rb

@@ -5,14 +5,15 @@
 #               Mitsuteru C. Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-#  $Id: test_soapwsdl.rb,v 1.4 2007/04/05 23:35:42 trevor Exp $ 
+#  $Id:$ 
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
-
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/io/soapwsdl'
 

data/test/functional/bio/io/test_togows.rb

@@ -8,10 +8,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'uri'
 require 'bio/version'
 require 'bio/io/togows'
@@ -23,8 +25,7 @@ module Bio
   # common tests for both instance methods and class methods
   module FuncTestTogoWSRESTcommon
 
-    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
-    TestData = Pathname.new(File.join(bioruby_root, 'test', 'data')).cleanpath.to_s
+    TestData = BioRubyTestDataPath
 
     def test_entry
       result = nil

data/test/functional/bio/sequence/test_output_embl.rb

@@ -5,15 +5,17 @@
 #               Jan Aerts <jan.aerts@bbsrc.ac.uk>
 # License::     The Ruby License
 #
-#  $Id: test_output_embl.rb,v 1.1.2.2 2008/03/28 00:56:27 ngoto Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
-require 'bio'
+require 'bio/sequence'
 
 module Bio
 class FuncTestSequenceOutputEMBL < Test::Unit::TestCase

data/test/functional/bio/test_command.rb

@@ -8,11 +8,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
-
+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 'tempfile'
 require 'bio/command'
@@ -23,8 +24,7 @@ module Bio
     def setup
       case RUBY_PLATFORM
       when /mswin32|bccwin32/
-        bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3)).cleanpath.to_s
-        cmd = File.expand_path(File.join(bioruby_root, 'test', 'data', 'command', 'echoarg2.bat'))
+        cmd = File.expand_path(File.join(BioRubyTestDataPath, 'command', 'echoarg2.bat'))
         @arg = [ cmd, 'test "argument 1"', '"test" argument 2', 'arg3' ]
         @expected = '"""test"" argument 2"'
       else
@@ -282,6 +282,55 @@ module Bio
     end
   end #class FuncTestCommandBackports
 
+  class FuncTestCommandTmpdir < Test::Unit::TestCase
+    def setup
+      if RUBY_VERSION < "1.8.3"
+        @notest = true
+      else
+        @notest = false
+      end
+    end
+
+    def test_initialize
+      return if @notest
+      tmpdir = Bio::Command::Tmpdir.new('bioruby')
+      assert_instance_of(Bio::Command::Tmpdir, tmpdir)
+      assert(File.directory?(tmpdir.path))
+      assert_nothing_raised {
+        # creates a dummy file
+        File.open(File.join(tmpdir.path, 'test'), 'w') do |w|
+          w.print "This is test."
+        end
+      }
+    end
+
+    def test_path
+      return if @notest
+      tmpdir = Bio::Command::Tmpdir.new('bioruby')
+      assert_kind_of(String, tmpdir.path)
+      assert(File.directory?(tmpdir.path))
+    end
+
+    def test_close!
+      return if @notest
+      tmpdir = Bio::Command::Tmpdir.new('bioruby')
+      path = tmpdir.path
+      # creates a dummy file
+      File.open(File.join(tmpdir.path, 'test'), 'w') do |w|
+        w.print "This is test."
+      end
+      assert_nothing_raised { tmpdir.close! }
+      assert_equal(false, File.directory?(path))
+    end
+
+    def test_path_after_close
+      return if @notest
+      tmpdir = Bio::Command::Tmpdir.new('bioruby')
+      tmpdir.close!
+      assert_raise(IOError) { tmpdir.path }
+    end
+  end #class FuncTestCommandTmpdir
+
   class FuncTestCommandNet < Test::Unit::TestCase
     def test_read_uri
       assert_nothing_raised {

data/test/runner.rb

@@ -1,10 +1,12 @@
 #!/usr/bin/env ruby
 
-require 'test/unit'
+# loading helper routine for testing bioruby
 require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), 
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
-bioruby_libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'], 'lib')).cleanpath.to_s
-$:.unshift(bioruby_libpath) unless $:.include?(bioruby_libpath)
+# libraries needed for the tests
+require 'test/unit'
 
 if !defined?(Test::Unit::AutoRunner) then
   # Ruby 1.9.1 does not have Test::Unit::AutoRunner

data/test/unit/bio/appl/bl2seq/test_report.rb

@@ -9,18 +9,19 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/bl2seq/report'
 
 
 module Bio
   class TestBl2seqReportData
-    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-    TestDataBl2seq = Pathname.new(File.join(bioruby_root, 'test', 'data', 'bl2seq')).cleanpath.to_s
+    TestDataBl2seq = Pathname.new(File.join(BioRubyTestDataPath, 'bl2seq')).cleanpath.to_s
 
     def self.output(format = 7)
       case format

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

@@ -7,10 +7,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/blast/ncbioptions'
 

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

@@ -9,10 +9,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/blast/report'
 
@@ -20,8 +22,7 @@ require 'bio/appl/blast/report'
 module Bio
 
   module TestBlastReportHelper
-    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-    TestDataBlast = Pathname.new(File.join(bioruby_root, 'test', 'data', 'blast')).cleanpath.to_s
+    TestDataBlast = Pathname.new(File.join(BioRubyTestDataPath, 'blast')).cleanpath.to_s
 
     private
 

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

@@ -8,10 +8,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'digest/sha1'
 require 'bio/io/flatfile'
@@ -19,8 +21,7 @@ require 'bio/appl/blast/rpsblast'
 
 module Bio
 module TestRPSBlast
-  bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-  TestFileName = Pathname.new(File.join(bioruby_root, 'test', 'data', 'rpsblast', 'misc.rpsblast')).cleanpath.to_s
+  TestFileName = Pathname.new(File.join(BioRubyTestDataPath, 'rpsblast', 'misc.rpsblast')).cleanpath.to_s
 
   class TestRPSBlastSplitter < Test::Unit::TestCase
     def setup

data/test/unit/bio/appl/gcg/test_msf.rb

@@ -7,10 +7,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/sequence'
 require 'bio/alignment'
@@ -21,9 +23,7 @@ module Bio
 
   module TestGCGMsfData
 
-    bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-
-    Filename_PileupAA = Pathname.new(File.join(bioruby_root, 'test', 'data', 'gcg', 'pileup-aa.msf')).cleanpath.to_s
+    Filename_PileupAA = Pathname.new(File.join(BioRubyTestDataPath, 'gcg', 'pileup-aa.msf')).cleanpath.to_s
 
     PileupAA = File.read(Filename_PileupAA).freeze
 

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

@@ -4,13 +4,15 @@
 # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_report.rb,v 1.4 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/genscan/report'
 
@@ -20,8 +22,7 @@ module Bio
   class TestGenscanReport < Test::Unit::TestCase
 
     def setup
-      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-      test_data = Pathname.new(File.join(bioruby_root, 'test', 'data', 'genscan')).cleanpath.to_s
+      test_data = Pathname.new(File.join(BioRubyTestDataPath, 'genscan')).cleanpath.to_s
       report = File.open(File.join(test_data, 'sample.report')).read
 
       @obj = Bio::Genscan::Report.new(report)
@@ -69,8 +70,7 @@ module Bio
   class TestGenscanReportGene < Test::Unit::TestCase
 
     def setup
-      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-      test_data = Pathname.new(File.join(bioruby_root, 'test', 'data', 'genscan')).cleanpath.to_s
+      test_data = Pathname.new(File.join(BioRubyTestDataPath, 'genscan')).cleanpath.to_s
       report = File.open(File.join(test_data, 'sample.report')).read
       @obj = Bio::Genscan::Report.new(report).predictions
     end
@@ -111,8 +111,7 @@ module Bio
   class TestGenscanReportExon < Test::Unit::TestCase
 
     def setup
-      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-      test_data = Pathname.new(File.join(bioruby_root, 'test', 'data', 'genscan')).cleanpath.to_s
+      test_data = Pathname.new(File.join(BioRubyTestDataPath, 'genscan')).cleanpath.to_s
       report = File.open(File.join(test_data, 'sample.report')).read
       @obj = Bio::Genscan::Report.new(report).predictions.first.exons.first
     end

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

@@ -7,10 +7,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/hmmer/report'
 
@@ -18,8 +20,7 @@ require 'bio/appl/hmmer/report'
 module Bio
 
   class TestHMMERReportData
-    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
-    TestDataHMMER = Pathname.new(File.join(bioruby_root, 'test', 'data', 'HMMER')).cleanpath.to_s
+    TestDataHMMER = Pathname.new(File.join(BioRubyTestDataPath, 'HMMER')).cleanpath.to_s
 
     def self.hmmpfam
       File.open(File.join(TestDataHMMER, 'hmmpfam.out')).read 

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

@@ -3,21 +3,22 @@
 #
 #   Copyright (C) 2006 Mitsuteru Nakao <n@bioruby.org>
 #
-#  $Id: test_report.rb,v 1.7 2007/07/18 11:11:57 nakao Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/appl/iprscan/report'
 
 
 module Bio
   class TestIprscanData
-    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), [".."] * 5)).cleanpath.to_s
-    TestDataIprscan = Pathname.new(File.join(bioruby_root, "test", "data", "iprscan")).cleanpath.to_s
+    TestDataIprscan = Pathname.new(File.join(BioRubyTestDataPath, "iprscan")).cleanpath.to_s
     def self.raw_format
       File.open(File.join(TestDataIprscan, "merged.raw"))
     end