search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/test/test_memory_leak.rb

@@ -0,0 +1,107 @@
+require "helper"
+
+class TestMemoryLeak < Nokogiri::TestCase
+
+  if ENV['NOKOGIRI_GC'] # turning these off by default for now
+
+    def test_dont_hurt_em_why
+      content = File.open("#{File.dirname(__FILE__)}/files/dont_hurt_em_why.xml").read
+      ndoc = Nokogiri::XML(content)
+      2.times do
+        ndoc.search('status text').first.inner_text
+        ndoc.search('user name').first.inner_text
+        GC.start
+      end
+    end
+    
+    class BadIO
+      def read(*args)
+        raise 'hell'
+      end
+      
+      def write(*args)
+        raise 'chickens'
+      end
+    end
+  
+    def test_for_mem_leak_on_io_callbacks
+      io = File.open SNUGGLES_FILE
+      reader = Nokogiri::XML.parse(io)
+
+      (10**10).times do
+        Nokogiri::XML.parse(BadIO.new) rescue nil
+        doc.write BadIO.new rescue nil
+      end
+    end
+
+    def test_for_memory_leak
+      begin
+        #  we don't use Dike in any tests, but requiring it has side effects
+        #  that can create memory leaks, and that's what we're testing for.
+        require 'rubygems'
+        require 'dike' # do not remove!
+
+        count_start = count_object_space_documents
+        xml_data = <<-EOS
+        <test>
+          <items>
+            <item>abc</item>
+            <item>1234</item>
+            <item>Zzz</item>
+          <items>
+        </test>
+        EOS
+        20.times do
+          doc = Nokogiri::XML(xml_data)
+          doc.xpath("//item")
+        end
+        2.times { GC.start }
+        count_end = count_object_space_documents
+        assert((count_end - count_start) <= 2, "memory leak detected")
+      rescue LoadError
+        puts "\ndike is not installed, skipping memory leak test"
+      end
+    end
+
+    if Nokogiri.ffi?
+      [ ['Node', 'p', nil],
+        ['CDATA', nil, 'content'],
+        ['Comment', nil, 'content'],
+        ['DocumentFragment', nil],
+        ['EntityReference', nil, 'p'],
+        ['ProcessingInstruction', nil, 'p', 'content'] ].each do |klass, *args|
+
+        define_method "test_for_leaked_#{klass}_nodes" do
+          Nokogiri::LibXML.expects(:xmlAddChild).at_least(1) # more than once shows we're GCing properly
+          10.times {
+            xml = Nokogiri::XML("<root></root>")
+            2.times { Nokogiri::XML.const_get(klass).new(*(args.collect{|arg| arg || xml})) }
+            GC.start
+          }
+          GC.start
+        end
+
+      end
+
+      def test_for_leaked_attr_nodes
+        Nokogiri::LibXML.expects(:xmlFreePropList).at_least(1) # more than once shows we're GCing properly
+        10.times {
+          xml = Nokogiri::XML("<root></root>")
+          2.times { Nokogiri::XML::Attr.new(xml, "p") }
+          GC.start
+        }
+        GC.start
+      end
+
+    end # if ffi
+
+  end # if NOKOGIRI_GC
+
+  private
+
+  def count_object_space_documents
+    count = 0
+    ObjectSpace.each_object {|j| count += 1 if j.is_a?(Nokogiri::XML::Document) }
+    count
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/test/test_nokogiri.rb

@@ -0,0 +1,138 @@
+require "helper"
+
+class TestNokogiri < Nokogiri::TestCase
+  def test_versions
+    version_match = /\d+\.\d+\.\d+/
+    assert_match version_match, Nokogiri::VERSION
+    assert_match version_match, Nokogiri::LIBXML_VERSION
+
+    if defined?(FFI) && defined?(Nokogiri::LibXML)
+      assert_equal 'ffi', Nokogiri::VERSION_INFO['libxml']['binding']
+      if RUBY_PLATFORM =~ /java/
+        assert_equal 'jruby', Nokogiri::VERSION_INFO['libxml']['platform']
+      else
+        assert_equal 'ruby', Nokogiri::VERSION_INFO['libxml']['platform']
+      end
+      assert Nokogiri.ffi?
+    else
+      assert_equal 'extension', Nokogiri::VERSION_INFO['libxml']['binding']
+
+      assert_match version_match, Nokogiri::VERSION_INFO['libxml']['compiled']
+      assert_equal Nokogiri::LIBXML_VERSION, Nokogiri::VERSION_INFO['libxml']['compiled']
+      assert ! Nokogiri.ffi?
+    end
+
+    assert_match version_match, Nokogiri::VERSION_INFO['libxml']['loaded']
+    Nokogiri::LIBXML_PARSER_VERSION =~ /(\d)(\d{2})(\d{2})/
+    major = $1.to_i
+    minor = $2.to_i
+    bug   = $3.to_i
+    assert_equal "#{major}.#{minor}.#{bug}", Nokogiri::VERSION_INFO['libxml']['loaded']
+  end
+
+  def test_libxml_iconv
+    assert Nokogiri.const_defined?(:LIBXML_ICONV_ENABLED)
+  end
+
+  def test_parse_with_io
+    doc = Nokogiri.parse(
+      StringIO.new("<html><head><title></title><body></body></html>")
+    )
+    assert_instance_of Nokogiri::HTML::Document, doc
+  end
+
+  def test_xml?
+    doc = Nokogiri.parse(File.read(XML_FILE))
+    assert doc.xml?
+    assert !doc.html?
+  end
+
+  def test_html?
+    doc = Nokogiri.parse(File.read(HTML_FILE))
+    assert !doc.xml?
+    assert doc.html?
+  end
+
+  def test_nokogiri_method_with_html
+    doc1 = Nokogiri(File.read(HTML_FILE))
+    doc2 = Nokogiri.parse(File.read(HTML_FILE))
+    assert_equal doc1.serialize, doc2.serialize
+  end
+
+  def test_nokogiri_method_with_block
+    doc = Nokogiri { b "bold tag" }
+    assert_equal('<b>bold tag</b>', doc.to_html.chomp)
+  end
+
+  def test_make_with_html
+    doc = Nokogiri.make("<b>bold tag</b>")
+    assert_equal('<b>bold tag</b>', doc.to_html.chomp)
+  end
+
+  def test_make_with_block
+    doc = Nokogiri.make { b "bold tag" }
+    assert_equal('<b>bold tag</b>', doc.to_html.chomp)
+  end
+
+  SLOP_HTML = <<-END
+  <html>
+    <body>
+      <ul>
+        <li class='red'>one</li>
+        <li class='blue'>two</li>
+      </ul>
+      <div>
+        one
+        <div>div two</div>
+      </div>
+    </body>
+  </html>
+  END
+
+  def test_slop_css
+    doc = Nokogiri::Slop(<<-eohtml)
+    <html>
+      <body>
+        <div>
+          one
+          <div class='foo'>
+            div two
+            <div class='foo'>
+              div three
+            </div>
+          </div>
+        </div>
+      </body>
+    </html>
+    eohtml
+    assert_equal "div", doc.html.body.div.div('.foo').name
+  end
+
+  def test_slop
+    doc = Nokogiri::Slop(SLOP_HTML)
+
+    assert_equal "one", doc.html.body.ul.li.first.text
+    assert_equal "two", doc.html.body.ul.li(".blue").text
+    assert_equal "div two", doc.html.body.div.div.text
+
+    assert_equal "two", doc.html.body.ul.li(:css => ".blue").text
+
+    assert_equal "two", doc.html.body.ul.li(:xpath => "position()=2").text
+    assert_equal "one", doc.html.body.ul.li(:xpath => ["contains(text(),'o')"]).first.text
+    assert_equal "two", doc.html.body.ul.li(:xpath => ["contains(text(),'o')","contains(text(),'t')"]).text
+
+    assert_raise(NoMethodError) { doc.nonexistent }
+  end
+
+  def test_slop_decorator
+    doc = Nokogiri(SLOP_HTML)
+    assert !doc.decorators(Nokogiri::XML::Node).include?(Nokogiri::Decorators::Slop)
+
+    doc.slop!
+    assert doc.decorators(Nokogiri::XML::Node).include?(Nokogiri::Decorators::Slop)
+
+    doc.slop!
+    assert_equal 1, doc.decorators(Nokogiri::XML::Node).select { |d| d == Nokogiri::Decorators::Slop }.size
+  end
+
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/test/test_reader.rb

@@ -0,0 +1,421 @@
+# -*- coding: utf-8 -*-
+require "helper"
+
+class TestReader < Nokogiri::TestCase
+  def test_from_io_sets_io_as_source
+    io = File.open SNUGGLES_FILE
+    reader = Nokogiri::XML::Reader.from_io(io)
+    assert_equal io, reader.source
+  end
+
+  def test_empty_element?
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+<xml><city>Paris</city><state/></xml>
+    eoxml
+
+    results = reader.map do |node|
+      if node.node_type == Nokogiri::XML::Node::ELEMENT_NODE
+        node.empty_element?
+      end
+    end
+    assert_equal [false, false, nil, nil, true, nil], results
+  end
+
+  def test_self_closing?
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+<xml><city>Paris</city><state/></xml>
+    eoxml
+
+    results = reader.map do |node|
+      if node.node_type == Nokogiri::XML::Node::ELEMENT_NODE
+        node.self_closing?
+      end
+    end
+    assert_equal [false, false, nil, nil, true, nil], results
+  end
+
+  def test_reader_takes_block
+    options = nil
+    Nokogiri::XML::Reader(File.read(XML_FILE), XML_FILE) do |cfg|
+      options = cfg
+      options.nonet.nowarning.dtdattr
+    end
+    assert options.nonet?
+    assert options.nowarning?
+    assert options.dtdattr?
+  end
+
+  def test_nil_raises
+    assert_raises(ArgumentError) {
+      Nokogiri::XML::Reader.from_memory(nil)
+    }
+    assert_raises(ArgumentError) {
+      Nokogiri::XML::Reader.from_io(nil)
+    }
+  end
+
+  def test_from_io
+    io = File.open SNUGGLES_FILE
+    reader = Nokogiri::XML::Reader.from_io(io)
+    assert_equal false, reader.default?
+    assert_equal [false, false, false, false, false, false, false],
+      reader.map { |x| x.default? }
+  end
+
+  def test_io
+    io = File.open SNUGGLES_FILE
+    reader = Nokogiri::XML::Reader(io)
+    assert_equal false, reader.default?
+    assert_equal [false, false, false, false, false, false, false],
+      reader.map { |x| x.default? }
+  end
+
+  def test_string_io
+    io = StringIO.new(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo awesome='true'>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    reader = Nokogiri::XML::Reader(io)
+    assert_equal false, reader.default?
+    assert_equal [false, false, false, false, false, false, false],
+      reader.map { |x| x.default? }
+  end
+  
+  class ReallyBadIO
+    def read(size)
+      'a' * size ** 10
+    end
+  end
+
+  unless Nokogiri.ffi?
+    def test_io_that_reads_too_much
+      io = ReallyBadIO.new
+      Nokogiri::XML::Reader(io)
+    end
+  end
+
+  def test_in_memory
+    assert Nokogiri::XML::Reader(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo awesome='true'>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+  end
+
+  def test_reader_holds_on_to_string
+    xml = <<-eoxml
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo awesome='true'>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    reader = Nokogiri::XML::Reader(xml)
+    if Nokogiri.ffi?
+      assert_not_nil reader.source
+      assert reader.source.is_a?(FFI::MemoryPointer)
+    else
+      assert_equal xml, reader.source
+    end
+  end
+
+  def test_default?
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo awesome='true'>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    assert_equal false, reader.default?
+    assert_equal [false, false, false, false, false, false, false],
+      reader.map { |x| x.default? }
+  end
+
+  def test_value?
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo awesome='true'>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    assert_equal false, reader.value?
+    assert_equal [false, true, false, true, false, true, false],
+      reader.map { |x| x.value? }
+  end
+
+  def test_read_error_document
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo awesome='true'>snuggles!</tenderlove:foo>
+      <foo>
+    </x>
+    eoxml
+    assert_raises(Nokogiri::XML::SyntaxError) do
+      reader.each { |node| }
+    end
+    assert 1, reader.errors.length
+  end
+
+  def test_attributes?
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo awesome='true'>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    assert_equal false, reader.attributes?
+    assert_equal [true, false, true, false, true, false, true],
+      reader.map { |x| x.attributes? }
+  end
+
+  def test_attributes
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'
+       xmlns='http://mothership.connection.com/'
+       >
+      <tenderlove:foo awesome='true'>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    assert_equal({}, reader.attributes)
+    assert_equal [{'xmlns:tenderlove'=>'http://tenderlovemaking.com/',
+                   'xmlns'=>'http://mothership.connection.com/'},
+                  {}, {"awesome"=>"true"}, {}, {"awesome"=>"true"}, {},
+                  {'xmlns:tenderlove'=>'http://tenderlovemaking.com/',
+                   'xmlns'=>'http://mothership.connection.com/'}],
+      reader.map { |x| x.attributes }
+  end
+
+  def test_attribute_roundtrip
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'
+       xmlns='http://mothership.connection.com/'
+       >
+      <tenderlove:foo awesome='true' size='giant'>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    reader.each do |node|
+      node.attributes.each do |key, value|
+        assert_equal value, node.attribute(key)
+      end
+    end
+  end
+
+  def test_attribute_at
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo awesome='true'>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    assert_nil reader.attribute_at(nil)
+    assert_nil reader.attribute_at(0)
+    assert_equal ['http://tenderlovemaking.com/', nil, 'true', nil, 'true', nil, 'http://tenderlovemaking.com/'],
+      reader.map { |x| x.attribute_at(0) }
+  end
+
+  def test_attribute
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo awesome='true'>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    assert_nil reader.attribute(nil)
+    assert_nil reader.attribute('awesome')
+    assert_equal [nil, nil, 'true', nil, 'true', nil, nil],
+      reader.map { |x| x.attribute('awesome') }
+  end
+
+  def test_attribute_length
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo awesome='true'>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    assert_equal 0, reader.attribute_count
+    assert_equal [1, 0, 1, 0, 0, 0, 0], reader.map { |x| x.attribute_count }
+  end
+
+  def test_depth
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    assert_equal 0, reader.depth
+    assert_equal [0, 1, 1, 2, 1, 1, 0], reader.map { |x| x.depth }
+  end
+
+  def test_encoding
+    string = <<-eoxml
+    <awesome>
+      <p xml:lang="en">The quick brown fox jumps over the lazy dog.</p>
+      <p xml:lang="ja">日本語が上手です</p>
+    </awesome>
+    eoxml
+    reader = Nokogiri::XML::Reader.from_memory(string, nil, 'UTF-8')
+    assert_equal ['UTF-8'], reader.map { |x| x.encoding }.uniq
+  end
+
+  def test_xml_version
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    assert_nil reader.xml_version
+    assert_equal ['1.0'], reader.map { |x| x.xml_version }.uniq
+  end
+
+  def test_lang
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <awesome>
+      <p xml:lang="en">The quick brown fox jumps over the lazy dog.</p>
+      <p xml:lang="ja">日本語が上手です</p>
+    </awesome>
+    eoxml
+    assert_nil reader.lang
+    assert_equal [nil, nil, "en", "en", "en", nil, "ja", "ja", "ja", nil, nil],
+      reader.map { |x| x.lang }
+  end
+
+  def test_value
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:tenderlove='http://tenderlovemaking.com/'>
+      <tenderlove:foo>snuggles!</tenderlove:foo>
+    </x>
+    eoxml
+    assert_nil reader.value
+    assert_equal [nil, "\n      ", nil, "snuggles!", nil, "\n    ", nil],
+      reader.map { |x| x.value }
+  end
+
+  def test_prefix
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:edi='http://ecommerce.example.org/schema'>
+      <edi:foo>hello</edi:foo>
+    </x>
+    eoxml
+    assert_nil reader.prefix
+    assert_equal [nil, nil, "edi", nil, "edi", nil, nil],
+      reader.map { |n| n.prefix }
+  end
+
+  def test_node_type
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x>
+      <y>hello</y>
+    </x>
+    eoxml
+    assert_equal 0, reader.node_type
+    assert_equal [1, 14, 1, 3, 15, 14, 15], reader.map { |n| n.node_type }
+  end
+
+  def test_inner_xml
+    str = "<x><y>hello</y></x>"
+    reader = Nokogiri::XML::Reader.from_memory(str)
+
+    reader.read
+
+    assert_equal "<y>hello</y>", reader.inner_xml
+  end
+
+  def test_outer_xml
+    str = "<x><y>hello</y></x>"
+    reader = Nokogiri::XML::Reader.from_memory(str)
+
+    reader.read
+
+    assert_equal str, reader.outer_xml
+  end
+
+  def test_state
+    reader = Nokogiri::XML::Reader.from_memory('<foo>bar</bar>')
+    assert reader.state
+  end
+
+  def test_ns_uri
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:edi='http://ecommerce.example.org/schema'>
+      <edi:foo>hello</edi:foo>
+    </x>
+    eoxml
+    assert_nil reader.namespace_uri
+    assert_equal([nil,
+                  nil,
+                  "http://ecommerce.example.org/schema",
+                  nil,
+                  "http://ecommerce.example.org/schema",
+                  nil,
+                  nil],
+                  reader.map { |n| n.namespace_uri })
+  end
+
+  def test_local_name
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:edi='http://ecommerce.example.org/schema'>
+      <edi:foo>hello</edi:foo>
+    </x>
+    eoxml
+    assert_nil reader.local_name
+    assert_equal(["x", "#text", "foo", "#text", "foo", "#text", "x"],
+                 reader.map { |n| n.local_name })
+  end
+
+  def test_name
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+    <x xmlns:edi='http://ecommerce.example.org/schema'>
+      <edi:foo>hello</edi:foo>
+    </x>
+    eoxml
+    assert_nil reader.name
+    assert_equal(["x", "#text", "edi:foo", "#text", "edi:foo", "#text", "x"],
+                 reader.map { |n| n.name })
+  end
+
+  def test_base_uri
+    reader = Nokogiri::XML::Reader.from_memory(<<-eoxml)
+      <x xml:base="http://base.example.org/base/">
+        <link href="link"/>
+        <other xml:base="http://other.example.org/"/>
+        <relative xml:base="relative">
+          <link href="stuff" />
+        </relative>
+      </x>
+    eoxml
+
+    assert_nil reader.base_uri
+    assert_equal(["http://base.example.org/base/",
+                  "http://base.example.org/base/",
+                  "http://base.example.org/base/",
+                  "http://base.example.org/base/",
+                  "http://other.example.org/",
+                  "http://base.example.org/base/",
+                  "http://base.example.org/base/relative",
+                  "http://base.example.org/base/relative",
+                  "http://base.example.org/base/relative",
+                  "http://base.example.org/base/relative",
+                  "http://base.example.org/base/relative",
+                  "http://base.example.org/base/",
+                  "http://base.example.org/base/"],
+                  reader.map {|n| n.base_uri })
+  end
+
+  def test_read_from_memory
+    called = false
+    reader = Nokogiri::XML::Reader.from_memory('<foo>bar</foo>')
+    reader.each do |node|
+      called = true
+      assert node
+    end
+    assert called
+  end
+
+  def test_large_document_smoke_test
+    #  simply run on a large document to verify that there no GC issues
+    xml = []
+    xml << "<elements>"
+    10000.times { |j| xml << "<element id=\"#{j}\"/>" }
+    xml << "</elements>"
+    xml = xml.join("\n")
+
+    Nokogiri::XML::Reader.from_memory(xml).each do |e|
+      e.attributes
+    end
+  end
+
+end