ngoto-bio 1.2.9.9501 → 1.3.0

data/lib/bio/version.rb

@@ -0,0 +1,25 @@
+#
+# = bio/version.rb - BioRuby version information
+#
+# Copyright::	Copyright (C) 2001-2009
+#		Toshiaki Katayama <k@bioruby.org>,
+#               Naohisa Goto <ng@bioruby.org>
+# License::	The Ruby License
+#
+
+module Bio
+
+  # BioRuby version (Array containing Integer)
+  BIORUBY_VERSION = [1, 3, 0].extend(Comparable).freeze
+
+  # Extra version specifier (String or nil).
+  # Existance of the value indicates pre-release version or modified version.
+  BIORUBY_EXTRA_VERSION = nil
+
+  # Version identifier, including extra version string (String)
+  # Unlike BIORUBY_VERSION, it is not comparable.
+  BIORUBY_VERSION_ID =
+    (BIORUBY_VERSION.join('.') + BIORUBY_EXTRA_VERSION.to_s).freeze
+
+end #module Bio
+

data/lib/bio.rb

@@ -10,7 +10,9 @@
 
 module Bio
 
-  BIORUBY_VERSION = [1, 3, 0].extend(Comparable)
+  autoload :BIORUBY_VERSION, 'bio/version'
+  autoload :BIORUBY_EXTRA_VERSION, 'bio/version'
+  autoload :BIORUBY_VERSION_ID, 'bio/version'
 
   ### Basic data types
 
@@ -182,6 +184,7 @@ module Bio
     autoload :REST,       'bio/io/ncbirest'
   end
 
+  autoload :TogoWS,       'bio/io/togows'
 
   ### Applications
 

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

@@ -0,0 +1,267 @@
+#
+# test/functional/bio/io/test_togows.rb - Functional test for Bio::TogoWS
+#
+# 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 'uri'
+require 'bio/version'
+require 'bio/io/togows'
+require 'bio/db/genbank/genbank'
+require 'test/unit'
+
+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
+
+    def test_entry
+      result = nil
+      acc = 'AF237819'
+      assert_nothing_raised {
+        result = @togows.entry('genbank', acc)
+      }
+      assert(!result.to_s.strip.empty?)
+      gb = Bio::GenBank.new(result)
+      assert(gb.accessions.include?(acc))
+    end
+
+    def test_entry_multi
+      result = nil
+      accs = [ 'AF237819' ,'AB302966', 'AY582120' ]
+      assert_nothing_raised {
+        result = @togows.entry('genbank', accs)
+      }
+      assert(!result.to_s.strip.empty?)
+      count = 0
+      accs.each do |x|
+        assert_match(Regexp.new(x), result)
+        count += 1
+      end
+      assert_equal(accs.size, count)
+
+      # argument is a string
+      accs2 = accs.join(',')
+      result2 = nil
+      assert_nothing_raised {
+        result2 = @togows.entry('genbank', accs2)
+      }
+      assert(result2 == result)
+    end
+
+    def test_entry_with_format
+      result = nil
+      acc = 'AF237819'
+      assert_nothing_raised {
+        result = @togows.entry('genbank', acc, 'fasta')
+      }
+      assert(!result.to_s.strip.empty?)
+      assert_match(/^\>/, result)
+    end
+
+    def test_entry_with_key
+      result = nil
+      assert_nothing_raised {
+        result = @togows.entry('pubmed', '16381885', nil, 'authors')
+      }
+      assert(!result.to_s.strip.empty?)
+    end
+
+    def test_entry_with_format_and_key
+      result = nil
+      assert_nothing_raised {
+        result = @togows.entry('pubmed', '16381885', 'json', 'authors')
+      }
+      assert(!result.to_s.strip.empty?)
+    end
+
+    def test_search
+      result = nil
+      assert_nothing_raised {
+        result = @togows.search('nuccore', 'Milnesium tardigradum')
+      }
+      assert(!result.to_s.strip.empty?)
+    end
+
+    def test_search_with_offset_limit
+      result = nil
+      assert_nothing_raised {
+        result = @togows.search('nuccore', 'Milnesium tardigradum', 2, 3)
+      }
+      assert(!result.to_s.strip.empty?)
+      ary = result.chomp.split(/\n/)
+      assert_equal(3, ary.size)
+    end
+
+    def test_search_with_offset_limit_format
+      result = nil
+      assert_nothing_raised {
+        result = @togows.search('nuccore', 'Milnesium tardigradum', 2, 3,
+                                'json')
+      }
+      assert(!result.to_s.strip.empty?)
+    end
+
+    def test_convert
+      data = File.read(File.join(TestData, 'blast', 'b0002.faa.m0'))
+      result = nil
+      assert_nothing_raised {
+        result = @togows.convert(data, 'blast', 'gff')
+      }
+      assert(!result.to_s.strip.empty?)
+    end
+
+    def test_retrieve
+      result = nil
+      assert_nothing_raised {
+        result = @togows.retrieve('AF237819')
+      }
+      assert(!result.to_s.strip.empty?)
+    end
+
+    def test_retrieve_1id_1db
+      result = nil
+      assert_nothing_raised {
+        result = @togows.retrieve('hsa:124',
+                                  :database => 'gene',
+                                  :field => 'entry_id',
+                                  :format => 'json')
+      }
+      assert(!result.to_s.strip.empty?)
+    end
+
+    def test_retrieve_1id_2db
+      result = nil
+      assert_nothing_raised {
+        result = @togows.retrieve('1.1.1.1',
+                                  :database => [ 'gene', 'enzyme' ])
+      }
+      assert(!result.to_s.strip.empty?)
+    end
+
+    def test_retrieve_2id_2db
+      result = nil
+      assert_nothing_raised {
+        result = @togows.retrieve([ '1.1.1.1', 'hsa:124' ],
+                                  :database => [ 'gene', 'enzyme' ])
+      }
+      assert(!result.to_s.strip.empty?)
+    end
+
+    def test_entry_database_list
+      result = nil
+      assert_nothing_raised {
+        result = @togows.entry_database_list
+      }
+      assert_kind_of(Array, result)
+      assert(!result.empty?)
+    end
+
+    def test_search_database_list
+      result = nil
+      assert_nothing_raised {
+        result = @togows.search_database_list
+      }
+      assert_kind_of(Array, result)
+      assert(!result.empty?)
+    end
+
+  end #FuncTestTogoWSRESTcommon
+
+  # functional test for Bio::TogoWS::REST
+  class FuncTestTogoWSREST < Test::Unit::TestCase
+
+    include FuncTestTogoWSRESTcommon
+
+    def setup
+      @togows = Bio::TogoWS::REST.new
+    end
+
+  end #class FuncTestTogoWSREST
+
+  # functional test for Bio::TogoWS::REST private methods
+  class FuncTestTogoWSRESTprivate < Test::Unit::TestCase
+
+    def setup
+      @togows = Bio::TogoWS::REST.new
+    end
+
+    def test_get
+      response = nil
+      acc = 'AF237819'
+      assert_nothing_raised {
+        response = @togows.instance_eval {
+          get('entry', 'genbank', acc, 'entry_id')
+        }
+      }
+      assert_kind_of(Net::HTTPResponse, response)
+      assert_equal("200", response.code)
+      result = response.body
+      assert(!result.to_s.strip.empty?)
+    end
+
+    def test_get_dir
+      response = nil
+      assert_nothing_raised {
+        response = @togows.instance_eval {
+          get_dir('search')
+        }
+      }
+      assert_kind_of(Net::HTTPResponse, response)
+      assert_equal("200", response.code)
+      result = response.body
+      assert(!result.to_s.strip.empty?)
+    end
+
+    def test_post_data
+      data = File.read(File.join(Bio::FuncTestTogoWSRESTcommon::TestData,
+                                 'blast', 'b0002.faa.m0'))
+      response = nil
+      assert_nothing_raised {
+        response = @togows.instance_eval {
+          post_data(data, 'convert', 'blast.gff')
+        }
+      }
+      assert_kind_of(Net::HTTPResponse, response)
+      assert_equal("200", response.code)
+      result = response.body
+      assert(!result.to_s.strip.empty?)
+    end
+
+    def test_database_list
+      result = nil
+      assert_nothing_raised {
+        result = @togows.instance_eval {
+          database_list('entry')
+        }
+      }
+      assert_kind_of(Array, result)
+      assert(!result.empty?)
+    end
+
+  end #class FuncTestTogoWSRESTprivate
+
+  if false # DISABLED because of the server load and execution time
+
+    # functional test for Bio::TogoWS::REST class methods
+    class FuncTestTogoWSRESTclassMethod < Test::Unit::TestCase
+      include FuncTestTogoWSRESTcommon
+      def setup
+        @togows = Bio::TogoWS::REST
+      end
+    end #class FuncTestTogoWSRESTclassMethod
+
+  end #if false
+
+end #module Bio

data/test/runner.rb

@@ -13,6 +13,13 @@ if !defined?(Test::Unit::AutoRunner) then
   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.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))

data/test/unit/bio/db/test_gff.rb

@@ -770,6 +770,10 @@ END_OF_DATA
       assert_equal(attr, @obj.attributes)
     end
 
+    def test_id
+      assert_equal('CEN1', @obj.id)
+    end
+
     def test_to_s
       str =<<END_OF_DATA
 chrI	SGD	centromere	151467	151584	.	+	.	ID=CEN1;Name=CEN1;gene=CEN1;Alias=CEN1,test%3B0001;Note=Chromosome I centromere;dbxref=SGD:S000006463;Target=test%2002 123 456 -,test%2C03 159 314;memo%3Dtest%3Battr=99.9%25%09match
@@ -848,6 +852,65 @@ END_OF_DATA
       assert_equal(1, obj.frame)
     end
 
+    def test_id_replace
+      data =<<END_OF_DATA
+ctg123	src	CDS	456	788	1e-10	-	2	ID=test03
+END_OF_DATA
+      obj = Bio::GFF::GFF3::Record.new(data)
+      assert_equal('test03', obj.id)
+      assert_equal('test_id', obj.id = 'test_id')
+      assert_equal('test_id', obj.id)
+    end
+
+    def test_id_set
+      data =<<END_OF_DATA
+ctg123	src	CDS	456	788	1e-10	-	2	NAME=test03
+END_OF_DATA
+      obj = Bio::GFF::GFF3::Record.new(data)
+      assert_nil(obj.id)
+      assert_equal('test_id', obj.id = 'test_id')
+      assert_equal('test_id', obj.id)
+      assert_equal('next_test', obj.id = 'next_test')
+      assert_equal('next_test', obj.id)
+    end
+
+    def test_id_multiple
+      # Note: Two ID attributes in a record is illegal in GFF3.
+      data =<<END_OF_DATA
+ctg123	src	CDS	456	788	.	-	2	ID=test03,test04
+END_OF_DATA
+      obj = Bio::GFF::GFF3::Record.new(data)
+      assert_equal([ [ 'ID', 'test03' ], [ 'ID', 'test04' ] ],
+                   obj.attributes)
+      assert_equal('test03', obj.id)
+      assert_equal('test_id', obj.id = 'test_id')
+      assert_equal('test_id', obj.id)
+      assert_equal([ [ 'ID', 'test_id' ], [ 'ID', 'test04' ] ],
+                   obj.attributes)
+      str = "ctg123\tsrc\tCDS\t456\t788\t.\t-\t2\tID=test_id,test04\n"
+      assert_equal(str, obj.to_s)
+    end
+
+    def test_id_multiple2
+      # Note: Two ID attributes in a record is illegal in GFF3.
+      data =<<END_OF_DATA
+ctg123	src	CDS	456	788	.	-	2	ID=test03;ID=test04
+END_OF_DATA
+      obj = Bio::GFF::GFF3::Record.new(data)
+      assert_equal([ [ 'ID', 'test03' ], [ 'ID', 'test04' ] ],
+                   obj.attributes)
+      assert_equal('test03', obj.id)
+      assert_equal('test_id', obj.id = 'test_id')
+      assert_equal('test_id', obj.id)
+      assert_equal([ [ 'ID', 'test_id' ], [ 'ID', 'test04' ] ],
+                   obj.attributes)
+
+      # The "XXX=test03;XXX=test04" is automatically changed to
+      # "XXX=test03,test04", as defined in the GFF3 spec.
+      str = "ctg123\tsrc\tCDS\t456\t788\t.\t-\t2\tID=test_id,test04\n"
+      assert_equal(str, obj.to_s)
+    end
+
     def test_initialize_9
       obj = Bio::GFF::GFF3::Record.new('test01',
                                        'testsrc',

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

@@ -0,0 +1,161 @@
+#
+# test/unit/bio/io/test_togows.rb - Unit test for Bio::TogoWS
+#
+# 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 'uri'
+require 'net/http'
+require 'bio/version'
+require 'bio/io/togows'
+require 'test/unit'
+
+module Bio
+
+  # unit test for Bio::TogoWS::REST
+  class TestTogoWSREST < Test::Unit::TestCase
+
+    def setup
+      @togows = Bio::TogoWS::REST.new
+    end
+
+    def test_debug_default
+      assert_equal(false, @togows.debug)
+    end
+
+    def test_debug
+      assert_equal(true, @togows.debug = true)
+      assert_equal(true, @togows.debug)
+      assert_equal(false, @togows.debug = false)
+      assert_equal(false, @togows.debug)
+      assert_equal(true, @togows.debug = true)
+      assert_equal(true, @togows.debug)
+    end
+
+    def test_internal_http
+      assert_kind_of(Net::HTTP, @togows.internal_http)
+    end
+
+  end #class TestTogoWSREST
+
+  # unit test for Bio::TogoWS::REST private methods
+  class TestTogoWSRESTprivate < Test::Unit::TestCase
+
+    def setup
+      @togows = Bio::TogoWS::REST.new
+    end
+
+    def test_make_path
+      a_and_q = {
+        '/ab/cde/fghi' => [ 'ab', 'cde', 'fghi' ],
+        '/a+b/a%2Bb/a%2Fb/a%26b/a%3Bb/a%2Cb/a%3Bb' =>
+        [ 'a b', 'a+b', 'a/b', 'a&b', 'a;b', 'a,b', 'a;b' ]
+      }
+      count = 0
+      a_and_q.each do |k,v|
+        assert_equal(k, @togows.instance_eval { make_path(v) })
+        count += 1
+      end
+      assert_equal(a_and_q.size, count)
+    end
+
+    def test_prepare_return_value
+      dummyclass = Struct.new(:code, :body)
+      dummy200 = dummyclass.new("200", "this is test")
+      assert_equal("this is test",
+                   @togows.instance_eval { prepare_return_value(dummy200) })
+      dummy404 = dummyclass.new("404", "not found")
+      assert_equal(nil,
+                   @togows.instance_eval { prepare_return_value(dummy404) })
+    end
+
+  end #class TestTogoWSRESTprivate
+
+
+  # unit test for Bio::TogoWS::REST class methods
+  class TestTogoWSRESTclassMethod < Test::Unit::TestCase
+
+    def test_new
+      assert_instance_of(Bio::TogoWS::REST, Bio::TogoWS::REST.new)
+    end
+
+    def test_new_with_uri_string
+      t = Bio::TogoWS::REST.new('http://localhost:1234/test')
+      assert_instance_of(Bio::TogoWS::REST, t)
+      http = t.internal_http
+      assert_equal('localhost', http.address)
+      assert_equal(1234, http.port)
+      assert_equal('/test/', t.instance_eval { @pathbase })
+    end
+
+    def test_new_with_uri_object
+      u = URI.parse('http://localhost:1234/test')
+      t = Bio::TogoWS::REST.new(u)
+      assert_instance_of(Bio::TogoWS::REST, t)
+      http = t.internal_http
+      assert_equal('localhost', http.address)
+      assert_equal(1234, http.port)
+      assert_equal('/test/', t.instance_eval { @pathbase })
+    end
+
+    def test_entry
+      assert_respond_to(Bio::TogoWS::REST, :entry)
+    end
+
+    def test_search
+      assert_respond_to(Bio::TogoWS::REST, :search)
+    end
+
+    def test_convert
+      assert_respond_to(Bio::TogoWS::REST, :convert)
+    end
+
+    def test_retrieve
+      assert_respond_to(Bio::TogoWS::REST, :retrieve)
+    end
+
+    def test_entry_database_list
+      assert_respond_to(Bio::TogoWS::REST, :entry_database_list)
+    end
+
+    def test_search_database_list
+      assert_respond_to(Bio::TogoWS::REST, :search_database_list)
+    end
+
+  end #class TestTogoWSRESTclassMethod
+
+  # dummy class for testing Bio::TogoWS::AccessWait
+  class DummyAccessWait
+    include Bio::TogoWS::AccessWait
+  end
+
+  # unit test for Bio::TogoWS::AccessWait (all methods are private)
+  class TestTogoWSAccessWait < Test::Unit::TestCase
+    def setup
+      @obj = DummyAccessWait.new
+    end
+    
+    def test_togows_access_wait
+      assert_kind_of(Numeric, @obj.instance_eval { togows_access_wait })
+
+      waits = 0
+      2.times { waits += @obj.instance_eval { togows_access_wait } }
+      assert(waits > 0)
+    end
+
+    def test_reset_togows_access_wait
+      assert_nothing_raised {
+        @obj.instance_eval { reset_togows_access_wait }
+      }
+    end
+  end #class TestTogoWSAccessWait
+
+end #module Bio

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: ngoto-bio
 version: !ruby/object:Gem::Version 
-  version: 1.2.9.9501
+  version: 1.3.0
 platform: ruby
 authors: 
 - BioRuby project
@@ -9,7 +9,7 @@ autorequire: bio
 bindir: bin
 cert_chain: []
 
-date: 2009-01-11 00:00:00 -08:00
+date: 2009-02-13 00:00:00 -08:00
 default_executable: bioruby
 dependencies: []
 
@@ -24,11 +24,11 @@ executables:
 extensions: []
 
 extra_rdoc_files: 
+- ChangeLog
 - KNOWN_ISSUES.rdoc
 - README.rdoc
 - README_DEV.rdoc
 - doc/Changes-1.3.rdoc
-- ChangeLog
 files: 
 - ChangeLog
 - KNOWN_ISSUES.rdoc
@@ -47,7 +47,10 @@ files:
 - doc/KEGG_API.rd
 - doc/KEGG_API.rd.ja
 - doc/Tutorial.rd
+- doc/Tutorial.rd.html
 - doc/Tutorial.rd.ja
+- doc/Tutorial.rd.ja.html
+- doc/bioruby.css
 - etc/bioinformatics/seqdatabase.ini
 - extconf.rb
 - lib/bio.rb
@@ -218,6 +221,7 @@ files:
 - lib/bio/io/registry.rb
 - lib/bio/io/soapwsdl.rb
 - lib/bio/io/sql.rb
+- lib/bio/io/togows.rb
 - lib/bio/location.rb
 - lib/bio/map.rb
 - lib/bio/pathway.rb
@@ -251,6 +255,7 @@ files:
 - lib/bio/shell/plugin/psort.rb
 - lib/bio/shell/plugin/seq.rb
 - lib/bio/shell/plugin/soap.rb
+- lib/bio/shell/plugin/togows.rb
 - lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
 - lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
 - lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml
@@ -306,6 +311,7 @@ files:
 - lib/bio/util/restriction_enzyme/single_strand_complement.rb
 - lib/bio/util/restriction_enzyme/string_formatting.rb
 - lib/bio/util/sirna.rb
+- lib/bio/version.rb
 - rdoc.zsh
 - sample/any2fasta.rb
 - sample/biofetch.rb
@@ -370,6 +376,7 @@ files:
 - test/functional/bio/appl/test_pts1.rb
 - test/functional/bio/io/test_ensembl.rb
 - test/functional/bio/io/test_soapwsdl.rb
+- test/functional/bio/io/test_togows.rb
 - test/functional/bio/sequence/test_output_embl.rb
 - test/functional/bio/test_command.rb
 - test/runner.rb
@@ -419,6 +426,7 @@ files:
 - test/unit/bio/io/test_fastacmd.rb
 - test/unit/bio/io/test_flatfile.rb
 - test/unit/bio/io/test_soapwsdl.rb
+- test/unit/bio/io/test_togows.rb
 - test/unit/bio/sequence/test_aa.rb
 - test/unit/bio/sequence/test_common.rb
 - test/unit/bio/sequence/test_compat.rb