bio 1.4.3.0001 → 1.5.0

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

@@ -1,53 +0,0 @@
-#
-# test/functional/bio/io/test_soapwsdl.rb - Functional test for SOAP/WSDL
-#
-# Copyright::   Copyright (C) 2005,2007
-#               Mitsuteru C. Nakao <n@bioruby.org>
-# License::     The Ruby License
-#
-#  $Id:$ 
-#
-
-# loading helper routine for testing bioruby
-require 'pathname'
-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'
-
-module Bio
-
-class FuncTestSOAPWSDL < Test::Unit::TestCase
-
-  def setup
-    @wsdl = 'http://www.ebi.ac.uk/xembl/XEMBL.wsdl'
-    @obj = Bio::SOAPWSDL.new(@wsdl)
-  end
-
-  def test_wsdl
-    assert_equal(@wsdl, @obj.wsdl)
-  end
-  
-  def test_set_wsdl
-    @obj.wsdl = 'http://soap.genome.jp/KEGG.wsdl'
-    assert_equal('http://soap.genome.jp/KEGG.wsdl', @obj.wsdl)
-  end
-
-  def test_log
-    assert_equal(nil, @obj.log)
-  end
-
-  def test_set_log
-    require 'stringio'
-    io = StringIO.new
-    @obj.log = io
-
-    assert_equal(StringIO, @obj.log.class)
-  end
-
-end
-
-end
-

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

@@ -1,81 +0,0 @@
-#
-# test/unit/bio/io/test_ddbjxml.rb - Unit test for DDBJ XML.
-#
-# Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
-# License::   The Ruby License
-#
-#  $Id:$ 
-#
-
-# loading helper routine for testing bioruby
-require 'pathname'
-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/ddbjxml'
-
-module Bio
-
-class TestDDBJXMLConstants < Test::Unit::TestCase
-
-  def test_constants
-    constants = ["DDBJ", "TxSearch", "ClustalW", "PML", "Gib", "Fasta", 
-                 "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
-    assert_equal("http://xml.nig.ac.jp/wsdl/", Bio::DDBJ::XML::BASE_URI)
-  end
-
-  def test_blast_server_rul
-    assert_equal("http://xml.nig.ac.jp/wsdl/Blast.wsdl", Bio::DDBJ::XML::Blast::SERVER_URI)
-  end
-
-  def test_clustalw_server_url
-    assert_equal("http://xml.nig.ac.jp/wsdl/ClustalW.wsdl", Bio::DDBJ::XML::ClustalW::SERVER_URI)
-  end
-
-  def test_ddbj_server_url
-    assert_equal("http://xml.nig.ac.jp/wsdl/DDBJ.wsdl", Bio::DDBJ::XML::DDBJ::SERVER_URI)
-  end
-
-  def test_fasta_server_url
-    assert_equal("http://xml.nig.ac.jp/wsdl/Fasta.wsdl", Bio::DDBJ::XML::Fasta::SERVER_URI)
-  end
-
-  def test_getentry_server_url
-    assert_equal("http://xml.nig.ac.jp/wsdl/GetEntry.wsdl", Bio::DDBJ::XML::GetEntry::SERVER_URI)
-  end
-
-  def test_gib_server_url
-    assert_equal("http://xml.nig.ac.jp/wsdl/Gib.wsdl", Bio::DDBJ::XML::Gib::SERVER_URI)
-  end
-
-  def test_gtop_server_url
-    assert_equal("http://xml.nig.ac.jp/wsdl/Gtop.wsdl", Bio::DDBJ::XML::Gtop::SERVER_URI)
-  end
-
-  def test_pml_server_url
-    assert_equal("http://xml.nig.ac.jp/wsdl/PML.wsdl", Bio::DDBJ::XML::PML::SERVER_URI)
-  end
-
-  def test_srs_server_url
-    assert_equal("http://xml.nig.ac.jp/wsdl/SRS.wsdl", Bio::DDBJ::XML::SRS::SERVER_URI)
-  end
-
-  def test_txsearch_server_url
-    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
-
-
-end

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

@@ -1,111 +0,0 @@
-#
-# = test/unit/bio/io/test_ensembl.rb - Unit test for Bio::Ensembl.
-#
-# Copyright::   Copyright (C) 2006, 2007
-#               Mitsuteru C. Nakao <n@bioruby.org>
-# License::     The Ruby License
-#
-# $Id:$
-#
-
-# loading helper routine for testing bioruby
-require 'pathname'
-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'
-
-# tests for ensembl.rb,v 1.4
-class TestEnsembl_v14 < Test::Unit::TestCase
-  def test_ensembl_url
-    assert_equal('http://www.ensembl.org', Bio::Ensembl::ENSEMBL_URL)
-  end
-  
-  def test_server
-    obj = Bio::Ensembl.new('Homo_sapiens')
-    assert_equal('http://www.ensembl.org', obj.server)
-  end
-
-  def test_organism
-    organism = 'Homo_sapiens'
-    obj = Bio::Ensembl.new(organism)
-    assert_equal(organism, obj.organism)
-  end
-  
-  def test_self_human
-    organism = 'Homo_sapiens'    
-    obj = Bio::Ensembl.human
-    assert_equal(organism, obj.organism)
-  end
-
-  def test_self_mouse
-    organism = 'Mus_musculus'
-    obj = Bio::Ensembl.mouse
-    assert_equal(organism, obj.organism)
-  end
-
-  def test_new_with_2_args
-    organism = 'Oryza_sativa'
-    server_url = 'http://www.gramene.org'
-    obj = Bio::Ensembl.new(organism, server_url)
-    assert_equal(organism, obj.organism)
-    assert_equal(server_url, obj.server)
-  end
-end
-
-
-class TestEnsembl < Test::Unit::TestCase
-  def test_server_name
-    assert_equal('http://www.ensembl.org', Bio::Ensembl::EBIServerURI)
-  end
-
-  def test_server_uri
-    assert_equal('http://www.ensembl.org', Bio::Ensembl.server_uri)
-  end
-  
-  def test_set_server_uri
-    host = 'http://localhost'
-    Bio::Ensembl.server_uri(host)
-    assert_equal(host, Bio::Ensembl.server_uri)
-  end
-end
-
-
-class TestEnsemblBase < Test::Unit::TestCase
-  def test_exportview
-    
-  end
-end
-
-class TestEnsemblBaseClient < Test::Unit::TestCase
-  def test_class
-
-  end
-end
-
-
-class TestEnsemblHuman < Test::Unit::TestCase
-  def test_organism
-    assert_equal("Homo_sapiens", Bio::Ensembl::Human::Organism)
-  end
-end
-
-class TestEnsemblMouse < Test::Unit::TestCase
-  def test_organism
-    assert_equal("Mus_musculus", Bio::Ensembl::Mouse::Organism)
-  end
-end
-
-
-class TestEnsemblOldStyleClient < Test::Unit::TestCase
-  class Rice < Bio::Ensembl::Base
-    Organism = 'Oryza_sativa'
-  end
-
-  def test_organism
-    assert_equal('Oryza_sativa', Rice::Organism)
-  end
-end
-  

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

@@ -1,33 +0,0 @@
-#
-# test/unit/bio/io/test_soapwsdl.rb - Unit test for SOAP/WSDL
-#
-# Copytight::   Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
-# License::     The Ruby License
-#
-#  $Id:$ 
-#
-
-# loading helper routine for testing bioruby
-require 'pathname'
-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'
-
-module Bio
-
-class TestSOAPWSDL < Test::Unit::TestCase
-
-  def setup
-    @obj = Bio::SOAPWSDL
-  end
-
-  def test_methods
-    methods = ['list_methods','wsdl', 'wsdl=', 'log', 'log=']
-    assert_equal(methods.sort, (@obj.instance_methods - Object.methods).sort.collect { |x| x.to_s })
-  end
-
-end
-end