RubyGems - search_biomodel - Versions diffs - 0.1.2 → 1.0.0 - Mend

search_biomodel 0.1.2 → 1.0.0

Files changed (1059) hide show

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/test/test_soap4r_sax.rb ADDED

@@ -0,0 +1,52 @@
+require "helper"
+module XSD
+  module XMLParser
+    class Parser
+      @factory_added = nil
+      class << self; attr_reader :factory_added; end
+      def self.add_factory o
+        @factory_added = o
+      end
+      def initialize *args
+        @charset = nil
+      end
+      def characters foo
+      end
+      def start_element *args
+      end
+      def end_element *args
+      end
+    end
+  end
+end
+require 'xsd/xmlparser/nokogiri'
+class TestSoap4rSax < Nokogiri::TestCase
+  def test_factory_added
+    assert_equal XSD::XMLParser::Nokogiri, XSD::XMLParser::Nokogiri.factory_added
+  end
+  def test_parse
+    o = Class.new(::XSD::XMLParser::Nokogiri) do
+      attr_accessor :element_started
+      def initialize *args
+        super
+        @element_started = false
+      end
+      def start_element *args
+        @element_started = true
+      end
+    end.new 'foo'
+    o.do_parse '<?xml version="1.0" ?><root xmlns="http://example.com/"/>'
+    assert o.element_started, 'element started'
+  end
+end

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

@@ -0,0 +1,193 @@
+require "helper"
+class TestXsltTransforms < Nokogiri::TestCase
+  def setup
+    @doc = Nokogiri::XML(File.open(XML_FILE))
+  end
+  if Nokogiri.uses_libxml?
+    def test_class_methods
+      style = Nokogiri::XSLT(File.read(XSLT_FILE))
+      assert result = style.apply_to(@doc, ['title', '"Grandma"'])
+      assert_match %r{<h1>Grandma</h1>}, result
+    end
+    def test_transform
+      assert style = Nokogiri::XSLT.parse(File.read(XSLT_FILE))
+      assert result = style.apply_to(@doc, ['title', '"Booyah"'])
+      assert_match %r{<h1>Booyah</h1>}, result
+      assert_match %r{<th.*Employee ID</th>}, result
+      assert_match %r{<th.*Name</th>}, result
+      assert_match %r{<th.*Position</th>}, result
+      assert_match %r{<th.*Salary</th>}, result
+      assert_match %r{<td>EMP0003</td>}, result
+      assert_match %r{<td>Margaret Martin</td>}, result
+      assert_match %r{<td>Computer Specialist</td>}, result
+      assert_match %r{<td>100,000</td>}, result
+      assert_no_match %r{Dallas|Texas}, result
+      assert_no_match %r{Female}, result
+      assert result = style.apply_to(@doc, ['title', '"Grandma"'])
+      assert_match %r{<h1>Grandma</h1>}, result
+      assert result = style.apply_to(@doc)
+      assert_match %r{<h1></h1>}, result
+    end
+    def test_transform_with_output_style
+      xslt = Nokogiri::XSLT(<<-eoxslt)
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<xsl:stylesheet version="1.0"
+xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
+<xsl:output method="text" version="1.0"
+encoding="iso-8859-1" indent="yes"/>
+<xsl:param name="title"/>
+<xsl:template match="/">
+  <html>
+  <body>
+    <xsl:for-each select="staff/employee">
+    <tr>
+      <td><xsl:value-of select="employeeId"/></td>
+      <td><xsl:value-of select="name"/></td>
+      <td><xsl:value-of select="position"/></td>
+      <td><xsl:value-of select="salary"/></td>
+    </tr>
+    </xsl:for-each>
+    </table>
+  </body>
+  </html>
+</xsl:template>
+</xsl:stylesheet>
+      eoxslt
+      assert_no_match(/<td>/, xslt.apply_to(@doc, ['title', 'foo']))
+    end
+    def test_transform_arg_error
+      assert style = Nokogiri::XSLT(File.read(XSLT_FILE))
+      assert_raises(TypeError) do
+        style.transform(@doc, :foo)
+      end
+    end
+    def test_transform_with_hash
+      assert style = Nokogiri::XSLT(File.read(XSLT_FILE))
+      result = style.transform(@doc, {'title' => '"Booyah"'})
+      assert result.html?
+      assert_equal "Booyah", result.at_css("h1").content
+    end
+    def test_transform2
+      assert style = Nokogiri::XSLT(File.open(XSLT_FILE))
+      assert result_doc = style.transform(@doc)
+      assert result_doc.html?
+      assert_equal "", result_doc.at_css("h1").content
+      assert style = Nokogiri::XSLT(File.read(XSLT_FILE))
+      assert result_doc = style.transform(@doc, ['title', '"Booyah"'])
+      assert result_doc.html?
+      assert_equal "Booyah", result_doc.at_css("h1").content
+      assert result_string = style.apply_to(@doc, ['title', '"Booyah"'])
+      assert_equal result_string, style.serialize(result_doc)
+    end
+    def test_transform_with_quote_params
+      assert style = Nokogiri::XSLT(File.open(XSLT_FILE))
+      assert result_doc = style.transform(@doc, Nokogiri::XSLT.quote_params(['title', 'Booyah']))
+      assert result_doc.html?
+      assert_equal "Booyah", result_doc.at_css("h1").content
+      assert style = Nokogiri::XSLT.parse(File.read(XSLT_FILE))
+      assert result_doc = style.transform(@doc, Nokogiri::XSLT.quote_params({'title' => 'Booyah'}))
+      assert result_doc.html?
+      assert_equal "Booyah", result_doc.at_css("h1").content
+    end
+    def test_quote_params
+      h = {
+        :sym   => %{xxx},
+        'str'  => %{"xxx"},
+        :sym2  => %{'xxx'},
+        'str2' => %{x'x'x},
+        :sym3  => %{x"x"x},
+      }
+      hh=h.dup
+      result_hash = Nokogiri::XSLT.quote_params(h)
+      assert_equal hh, h # non-destructive
+      a=h.to_a.flatten
+      result_array = Nokogiri::XSLT.quote_params(a)
+      assert_equal h.to_a.flatten, a #non-destructive
+      assert_equal  result_array, result_hash
+    end
+    if Nokogiri.uses_libxml? # By now, cannot get it working on JRuby.
+      def test_exslt
+        assert doc = Nokogiri::XML.parse(File.read(EXML_FILE))
+        assert doc.xml?
+        assert style = Nokogiri::XSLT.parse(File.read(EXSLT_FILE))
+        params = {
+          :p1 => 'xxx',
+          :p2 => "x'x'x",
+          :p3 => 'x"x"x',
+          :p4 => '"xxx"'
+        }
+        result_doc = Nokogiri::XML.parse(style.apply_to(doc,
+            Nokogiri::XSLT.quote_params(params)))
+        assert_equal 'func-result', result_doc.at('/root/function').content
+        assert_equal 3, result_doc.at('/root/max').content.to_i
+        assert_match(
+          /\d{4}-\d\d-\d\d([-|+]\d\d:\d\d)?/,
+          result_doc.at('/root/date').content
+          )
+        result_doc.xpath('/root/params/*').each do  |p|
+          assert_equal p.content, params[p.name.intern]
+        end
+        check_params result_doc, params
+        result_doc = Nokogiri::XML.parse(style.apply_to(doc,
+            Nokogiri::XSLT.quote_params(params.to_a.flatten)))
+        check_params result_doc, params
+      end
+    end
+    def test_xslt_parse_error
+      xslt_str = <<-EOX
+<xsl:stylesheet version="1.0"
+ xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
+  <!-- Not well-formed: -->
+  <xsl:template match="/"/>
+    <values>
+      <xsl:for-each select="//*">
+        <value>
+          <xsl:value-of select="@id"/>
+        </value>
+      </xsl:for-each>
+    </values>
+  </xsl:template>
+</xsl:stylesheet>}
+      EOX
+      assert_raises(RuntimeError) { Nokogiri::XSLT.parse(xslt_str) }
+    end
+    def test_passing_a_non_document_to_transform
+      xsl = Nokogiri::XSLT('<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"></xsl:stylesheet>')
+      assert_raises(ArgumentError) { xsl.transform("<div></div>") }
+      assert_raises(ArgumentError) { xsl.transform(Nokogiri::HTML("").css("body")) }
+    end
+    def check_params result_doc, params
+      result_doc.xpath('/root/params/*').each do  |p|
+        assert_equal p.content, params[p.name.intern]
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/test/xml/node/test_save_options.rb ADDED

@@ -0,0 +1,20 @@
+require "helper"
+module Nokogiri
+  module XML
+    class Node
+      class TestSaveOptions < Nokogiri::TestCase
+        SaveOptions.constants.each do |constant|
+          class_eval %{
+            def test_predicate_#{constant.downcase}
+              options = SaveOptions.new(SaveOptions::#{constant})
+              assert options.#{constant.downcase}?
+              assert SaveOptions.new.#{constant.downcase}.#{constant.downcase}?
+            end
+          }
+        end
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/test/xml/node/test_subclass.rb ADDED

@@ -0,0 +1,44 @@
+require "helper"
+module Nokogiri
+  module XML
+    class Node
+      class TestSubclass < Nokogiri::TestCase
+        {
+          Nokogiri::XML::CDATA                  => 'doc, "foo"',
+          Nokogiri::XML::Attr                   => 'doc, "foo"',
+          Nokogiri::XML::Comment                => 'doc, "foo"',
+          Nokogiri::XML::EntityReference        => 'doc, "foo"',
+          Nokogiri::XML::ProcessingInstruction  => 'doc, "foo", "bar"',
+          Nokogiri::XML::DocumentFragment       => 'doc',
+          Nokogiri::XML::Node                   => '"foo", doc',
+          Nokogiri::XML::Text                   => '"foo", doc',
+        }.each do |klass, constructor|
+          class_eval %{
+            def test_subclass_#{klass.name.gsub('::', '_')}
+              doc = Nokogiri::XML::Document.new
+              klass = Class.new(#{klass.name})
+              node = klass.new(#{constructor})
+              assert_instance_of klass, node
+            end
+          }
+          class_eval <<-eocode, __FILE__, __LINE__ + 1
+            def test_subclass_initialize_#{klass.name.gsub('::', '_')}
+              doc = Nokogiri::XML::Document.new
+              klass = Class.new(#{klass.name}) do
+                attr_accessor :initialized_with
+                def initialize *args
+                  @initialized_with = args
+                end
+              end
+              node = klass.new(#{constructor}, 1)
+              assert_equal [#{constructor}, 1], node.initialized_with
+            end
+          eocode
+        end
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/test/xml/sax/test_parser.rb ADDED

@@ -0,0 +1,331 @@
+# -*- coding: utf-8 -*-
+require "helper"
+module Nokogiri
+  module XML
+    module SAX
+      class TestParser < Nokogiri::SAX::TestCase
+        def setup
+          super
+          @parser = XML::SAX::Parser.new(Doc.new)
+        end
+        def test_parser_context_yielded_io
+          doc = Doc.new
+          parser = XML::SAX::Parser.new doc
+          xml = "<foo a='&amp;b'/>"
+          block_called = false
+          parser.parse(StringIO.new(xml)) { |ctx|
+            block_called = true
+            ctx.replace_entities = true
+          }
+          assert block_called
+          assert_equal [['foo', [['a', '&b']]]], doc.start_elements
+        end
+        def test_parser_context_yielded_in_memory
+          doc = Doc.new
+          parser = XML::SAX::Parser.new doc
+          xml = "<foo a='&amp;b'/>"
+          block_called = false
+          parser.parse(xml) { |ctx|
+            block_called = true
+            ctx.replace_entities = true
+          }
+          assert block_called
+          assert_equal [['foo', [['a', '&b']]]], doc.start_elements
+        end
+        def test_xml_decl
+          {
+            ''          => nil,
+            '<?xml version="1.0" ?>'                  => ['1.0'],
+            '<?xml version="1.0" encoding="UTF-8" ?>' => ['1.0', 'UTF-8'],
+            '<?xml version="1.0" standalone="yes"?>'  => ['1.0', 'yes'],
+            '<?xml version="1.0" standalone="no"?>'   => ['1.0', 'no'],
+          }.each do |decl,value|
+            parser = XML::SAX::Parser.new(Doc.new)
+            xml = "#{decl}\n<root />"
+            parser.parse xml
+            assert parser.document.start_document_called, xml
+            assert_equal value, parser.document.xmldecls, xml
+          end
+        end
+        def test_parse_empty
+          assert_raises RuntimeError do
+            @parser.parse('')
+          end
+        end
+        def test_namespace_declaration_order_is_saved
+          @parser.parse <<-eoxml
+<root xmlns:foo='http://foo.example.com/' xmlns='http://example.com/'>
+  <a foo:bar='hello' />
+</root>
+          eoxml
+          assert_equal 2, @parser.document.start_elements_namespace.length
+          el = @parser.document.start_elements_namespace.first
+          namespaces = el.last
+          assert_equal ['foo', 'http://foo.example.com/'], namespaces.first
+          assert_equal [nil, 'http://example.com/'], namespaces.last
+        end
+        def test_bad_document_calls_error_handler
+          @parser.parse('<foo><bar></foo>')
+          assert @parser.document.errors
+          assert @parser.document.errors.length > 0
+        end
+        def test_namespace_are_super_fun_to_parse
+          @parser.parse <<-eoxml
+<root xmlns:foo='http://foo.example.com/'>
+  <a foo:bar='hello' />
+  <b xmlns:foo='http://bar.example.com/'>
+    <a foo:bar='hello' />
+  </b>
+  <foo:bar>hello world</foo:bar>
+</root>
+          eoxml
+          assert @parser.document.start_elements_namespace.length > 0
+          el = @parser.document.start_elements_namespace[1]
+          assert_equal 'a', el.first
+          assert_equal 1, el[1].length
+          attribute = el[1].first
+          assert_equal 'bar', attribute.localname
+          assert_equal 'foo', attribute.prefix
+          assert_equal 'hello', attribute.value
+          assert_equal 'http://foo.example.com/', attribute.uri
+        end
+        def test_sax_v1_namespace_attribute_declarations
+          @parser.parse <<-eoxml
+<root xmlns:foo='http://foo.example.com/' xmlns='http://example.com/'>
+  <a foo:bar='hello' />
+  <b xmlns:foo='http://bar.example.com/'>
+    <a foo:bar='hello' />
+  </b>
+  <foo:bar>hello world</foo:bar>
+</root>
+          eoxml
+          assert @parser.document.start_elements.length > 0
+          elm = @parser.document.start_elements.first
+          assert_equal 'root', elm.first
+          assert elm[1].include?(['xmlns:foo', 'http://foo.example.com/'])
+          assert elm[1].include?(['xmlns', 'http://example.com/'])
+        end
+        def test_sax_v1_namespace_nodes
+          @parser.parse <<-eoxml
+<root xmlns:foo='http://foo.example.com/' xmlns='http://example.com/'>
+  <a foo:bar='hello' />
+  <b xmlns:foo='http://bar.example.com/'>
+    <a foo:bar='hello' />
+  </b>
+  <foo:bar>hello world</foo:bar>
+</root>
+          eoxml
+          assert_equal 5, @parser.document.start_elements.length
+          assert @parser.document.start_elements.map { |se|
+            se.first
+          }.include?('foo:bar')
+          assert @parser.document.end_elements.map { |se|
+            se.first
+          }.include?('foo:bar')
+        end
+        def test_start_is_called_without_namespace
+          @parser.parse('<foo:f><bar></foo:f>')
+          assert_equal ['foo:f', 'bar'],
+            @parser.document.start_elements.map { |x| x.first }
+        end
+        def test_parser_sets_encoding
+          parser = XML::SAX::Parser.new(Doc.new, 'UTF-8')
+          assert_equal 'UTF-8', parser.encoding
+        end
+        def test_errors_set_after_parsing_bad_dom
+          doc = Nokogiri::XML('<foo><bar></foo>')
+          assert doc.errors
+          @parser.parse('<foo><bar></foo>')
+          assert @parser.document.errors
+          assert @parser.document.errors.length > 0
+          if RUBY_VERSION =~ /^1\.9/
+            doc.errors.each do |error|
+              assert_equal 'UTF-8', error.message.encoding.name
+            end
+          end
+          assert_equal doc.errors.length, @parser.document.errors.length
+        end
+        def test_parse_with_memory_argument
+          @parser.parse(File.read(XML_FILE))
+          assert(@parser.document.cdata_blocks.length > 0)
+        end
+        def test_parse_with_io_argument
+          File.open(XML_FILE, 'rb') { |f|
+            @parser.parse(f)
+          }
+          assert(@parser.document.cdata_blocks.length > 0)
+        end
+        def test_parse_io
+          File.open(XML_FILE, 'rb') { |f|
+            @parser.parse_io(f, 'UTF-8')
+          }
+          assert(@parser.document.cdata_blocks.length > 0)
+          if RUBY_VERSION =~ /^1\.9/
+            called = false
+            @parser.document.start_elements.flatten.each do |thing|
+              assert_equal 'UTF-8', thing.encoding.name
+              called = true
+            end
+            assert called
+            called = false
+            @parser.document.end_elements.flatten.each do |thing|
+              assert_equal 'UTF-8', thing.encoding.name
+              called = true
+            end
+            assert called
+            called = false
+            @parser.document.data.each do |thing|
+              assert_equal 'UTF-8', thing.encoding.name
+              called = true
+            end
+            assert called
+            called = false
+            @parser.document.comments.flatten.each do |thing|
+              assert_equal 'UTF-8', thing.encoding.name
+              called = true
+            end
+            assert called
+            called = false
+            @parser.document.cdata_blocks.flatten.each do |thing|
+              assert_equal 'UTF-8', thing.encoding.name
+              called = true
+            end
+            assert called
+          end
+        end
+        def test_parse_file
+          @parser.parse_file(XML_FILE)
+          assert_raises(ArgumentError) {
+            @parser.parse_file(nil)
+          }
+          assert_raises(Errno::ENOENT) {
+            @parser.parse_file('')
+          }
+          assert_raises(Errno::EISDIR) {
+            @parser.parse_file(File.expand_path(File.dirname(__FILE__)))
+          }
+        end
+        def test_render_parse_nil_param
+          assert_raises(ArgumentError) { @parser.parse_memory(nil) }
+        end
+        def test_ctag
+          @parser.parse_memory(<<-eoxml)
+            <p id="asdfasdf">
+              <![CDATA[ This is a comment ]]>
+              Paragraph 1
+            </p>
+          eoxml
+          assert_equal [' This is a comment '], @parser.document.cdata_blocks
+        end
+        def test_comment
+          @parser.parse_memory(<<-eoxml)
+            <p id="asdfasdf">
+              <!-- This is a comment -->
+              Paragraph 1
+            </p>
+          eoxml
+          assert_equal [' This is a comment '], @parser.document.comments
+        end
+        def test_characters
+          @parser.parse_memory(<<-eoxml)
+            <p id="asdfasdf">Paragraph 1</p>
+          eoxml
+          assert_equal ['Paragraph 1'], @parser.document.data
+        end
+        def test_end_document
+          @parser.parse_memory(<<-eoxml)
+            <p id="asdfasdf">Paragraph 1</p>
+          eoxml
+          assert @parser.document.end_document_called
+        end
+        def test_end_element
+          @parser.parse_memory(<<-eoxml)
+            <p id="asdfasdf">Paragraph 1</p>
+          eoxml
+          assert_equal [["p"]],
+            @parser.document.end_elements
+        end
+        def test_start_element_attrs
+          @parser.parse_memory(<<-eoxml)
+            <p id="asdfasdf">Paragraph 1</p>
+          eoxml
+          assert_equal [["p", [["id", "asdfasdf"]]]],
+                       @parser.document.start_elements
+        end
+        def test_start_element_attrs_include_namespaces
+          @parser.parse_memory(<<-eoxml)
+            <p xmlns:foo='http://foo.example.com/'>Paragraph 1</p>
+          eoxml
+          assert_equal [["p", [['xmlns:foo', 'http://foo.example.com/']]]],
+                       @parser.document.start_elements
+        end
+        def test_parse_document
+          @parser.parse_memory(<<-eoxml)
+            <p>Paragraph 1</p>
+            <p>Paragraph 2</p>
+          eoxml
+        end
+        def test_parser_attributes
+          xml = <<-eoxml
+<?xml version="1.0" ?><root><foo a="&amp;b" c="&gt;d" /></root>
+          eoxml
+          block_called = false
+          @parser.parse(xml) { |ctx|
+            block_called = true
+            ctx.replace_entities = true
+          }
+          assert block_called
+          assert_equal [['root', []], ['foo', [['a', '&b'], ['c', '>d']]]], @parser.document.start_elements
+        end
+      end
+    end
+  end
+end