search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib/nokogiri/xml/sax/parser_context.rb

@@ -0,0 +1,16 @@
+module Nokogiri
+  module XML
+    module SAX
+      ###
+      # Context for XML SAX parsers.  This class is usually not instantiated
+      # by the user.  Instead, you should be looking at
+      # Nokogiri::XML::SAX::Parser
+      class ParserContext
+        def self.new thing, encoding = 'UTF-8'
+          [:read, :close].all? { |x| thing.respond_to?(x) } ?
+            io(thing, Parser::ENCODINGS[encoding]) : memory(thing)
+        end
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib/nokogiri/xml/sax/push_parser.rb

@@ -0,0 +1,60 @@
+module Nokogiri
+  module XML
+    module SAX
+      ###
+      # PushParser can parse a document that is fed to it manually.  It
+      # must be given a SAX::Document object which will be called with
+      # SAX events as the document is being parsed.
+      #
+      # Calling PushParser#<< writes XML to the parser, calling any SAX
+      # callbacks it can.
+      #
+      # PushParser#finish tells the parser that the document is finished
+      # and calls the end_document SAX method.
+      #
+      # Example:
+      #
+      #   parser = PushParser.new(Class.new(XML::SAX::Document) {
+      #     def start_document
+      #       puts "start document called"
+      #     end
+      #   }.new)
+      #   parser << "<div>hello<"
+      #   parser << "/div>"
+      #   parser.finish
+      class PushParser
+
+        # The Nokogiri::XML::SAX::Document on which the PushParser will be
+        # operating
+        attr_accessor :document
+
+        ###
+        # Create a new PushParser with +doc+ as the SAX Document, providing
+        # an optional +file_name+ and +encoding+
+        def initialize(doc = XML::SAX::Document.new, file_name = nil, encoding = 'UTF-8')
+          @document = doc
+          @encoding = encoding
+          @sax_parser = XML::SAX::Parser.new(doc)
+
+          ## Create our push parser context
+          initialize_native(@sax_parser, file_name)
+        end
+
+        ###
+        # Write a +chunk+ of XML to the PushParser.  Any callback methods
+        # that can be called will be called immediately.
+        def write chunk, last_chunk = false
+          native_write(chunk, last_chunk)
+        end
+        alias :<< :write
+
+        ###
+        # Finish the parsing.  This method is only necessary for
+        # Nokogiri::XML::SAX::Document#end_document to be called.
+        def finish
+          write '', true
+        end
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib/nokogiri/xml/schema.rb

@@ -0,0 +1,63 @@
+module Nokogiri
+  module XML
+    class << self
+      ###
+      # Create a new Nokogiri::XML::Schema object using a +string_or_io+
+      # object.
+      def Schema string_or_io
+        Schema.new(string_or_io)
+      end
+    end
+
+    ###
+    # Nokogiri::XML::Schema is used for validating XML against a schema
+    # (usually from an xsd file).
+    #
+    # == Synopsis
+    #
+    # Validate an XML document against a Schema.  Loop over the errors that
+    # are returned and print them out:
+    #
+    #   xsd = Nokogiri::XML::Schema(File.read(PO_SCHEMA_FILE))
+    #   doc = Nokogiri::XML(File.read(PO_XML_FILE))
+    #
+    #   xsd.validate(doc).each do |error|
+    #     puts error.message
+    #   end
+    #
+    # The list of errors are Nokogiri::XML::SyntaxError objects.
+    class Schema
+      # Errors while parsing the schema file
+      attr_accessor :errors
+
+      ###
+      # Create a new Nokogiri::XML::Schema object using a +string_or_io+
+      # object.
+      def self.new string_or_io
+        from_document Nokogiri::XML(string_or_io)
+      end
+
+      ###
+      # Validate +thing+ against this schema.  +thing+ can be a
+      # Nokogiri::XML::Document object, or a filename.  An Array of
+      # Nokogiri::XML::SyntaxError objects found while validating the
+      # +thing+ is returned.
+      def validate thing
+        if thing.is_a?(Nokogiri::XML::Document) 
+          validate_document(thing) 
+        elsif File.file?(thing)
+          validate_file(thing)
+        else
+          raise ArgumentError, "Must provide Nokogiri::Xml::Document or the name of an existing file"
+        end
+      end
+
+      ###
+      # Returns true if +thing+ is a valid Nokogiri::XML::Document or
+      # file.
+      def valid? thing
+        validate(thing).length == 0
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib/nokogiri/xml/syntax_error.rb

@@ -0,0 +1,47 @@
+module Nokogiri
+  module XML
+    ###
+    # This class provides information about XML SyntaxErrors.  These
+    # exceptions are typically stored on Nokogiri::XML::Document#errors.
+    class SyntaxError < ::Nokogiri::SyntaxError
+      attr_reader :domain
+      attr_reader :code
+      attr_reader :level
+      attr_reader :file
+      attr_reader :line
+      attr_reader :str1
+      attr_reader :str2
+      attr_reader :str3
+      attr_reader :int1
+      attr_reader :column
+
+      ###
+      # return true if this is a non error
+      def none?
+        level == 0
+      end
+
+      ###
+      # return true if this is a warning
+      def warning?
+        level == 1
+      end
+
+      ###
+      # return true if this is an error
+      def error?
+        level == 2
+      end
+
+      ###
+      # return true if this error is fatal
+      def fatal?
+        level == 3
+      end
+
+      def to_s
+        super.chomp
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib/nokogiri/xml/text.rb

@@ -0,0 +1,9 @@
+module Nokogiri
+  module XML
+    class Text < Nokogiri::XML::CharacterData
+      def content=(string)
+        self.native_content = string.to_s
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib/nokogiri/xml/xpath.rb

@@ -0,0 +1,10 @@
+require 'nokogiri/xml/xpath/syntax_error'
+
+module Nokogiri
+  module XML
+    class XPath
+      # The Nokogiri::XML::Document tied to this XPath instance
+      attr_accessor :document
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib/nokogiri/xml/xpath/syntax_error.rb

@@ -0,0 +1,11 @@
+module Nokogiri
+  module XML
+    class XPath
+      class SyntaxError < XML::SyntaxError
+        def to_s
+          [super.chomp, str1].compact.join(': ')
+        end
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib/nokogiri/xml/xpath_context.rb

@@ -0,0 +1,16 @@
+module Nokogiri
+  module XML
+    class XPathContext
+
+      ###
+      # Register namespaces in +namespaces+
+      def register_namespaces(namespaces)
+        namespaces.each do |k, v|
+          k = k.gsub(/.*:/,'') # strip off 'xmlns:' or 'xml:'
+          register_ns(k, v)
+        end
+      end
+
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib/nokogiri/xslt.rb

@@ -0,0 +1,52 @@
+require 'nokogiri/xslt/stylesheet'
+
+module Nokogiri
+  class << self
+    ###
+    # Create a Nokogiri::XSLT::Stylesheet with +stylesheet+.
+    #
+    # Example:
+    #
+    #   xslt = Nokogiri::XSLT(File.read(ARGV[0]))
+    #
+    def XSLT stylesheet, modules = {}
+      XSLT.parse(stylesheet, modules)
+    end
+  end
+
+  ###
+  # See Nokogiri::XSLT::Stylesheet for creating and maniuplating
+  # Stylesheet object.
+  module XSLT
+    class << self
+      ###
+      # Parse the stylesheet in +string+, register any +modules+
+      def parse string, modules = {}
+        modules.each do |url, klass|
+          XSLT.register url, klass
+	end
+
+        Stylesheet.parse_stylesheet_doc(XML.parse(string))
+      end
+
+      ###
+      # Quote parameters in +params+ for stylesheet safety
+      def quote_params params
+        parray = (params.instance_of?(Hash) ? params.to_a.flatten : params).dup
+        parray.each_with_index do |v,i|
+          if i % 2 > 0
+            parray[i]=
+              if v =~ /'/
+                "concat('#{ v.gsub(/'/, %q{', "'", '}) }')"
+              else
+                "'#{v}'";
+              end
+          else
+            parray[i] = v.to_s
+          end
+        end
+        parray.flatten
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib/nokogiri/xslt/stylesheet.rb

@@ -0,0 +1,25 @@
+module Nokogiri
+  module XSLT
+    ###
+    # A Stylesheet represents an XSLT Stylesheet object.  Stylesheet creation
+    # is done through Nokogiri.XSLT.  Here is an example of transforming
+    # an XML::Document with a Stylesheet:
+    #
+    #   doc   = Nokogiri::XML(File.read('some_file.xml'))
+    #   xslt  = Nokogir::XSLT(File.read('some_transformer.xslt'))
+    #
+    #   puts xslt.transform(doc)
+    #
+    # See Nokogiri::XSLT::Stylesheet#transform for more transformation
+    # information.
+    class Stylesheet
+      ###
+      # Apply an XSLT stylesheet to an XML::Document.
+      # +params+ is an array of strings used as XSLT parameters.
+      # returns serialized document
+      def apply_to document, params = []
+        serialize(transform(document, params))
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib/xsd/xmlparser/nokogiri.rb

@@ -0,0 +1,90 @@
+require 'nokogiri'
+
+module XSD # :nodoc:
+  module XMLParser # :nodoc:
+    ###
+    # Nokogiri XML parser for soap4r.
+    #
+    # Nokogiri may be used as the XML parser in soap4r.  Simply require
+    # 'xsd/xmlparser/nokogiri' in your soap4r applications, and soap4r
+    # will use Nokogiri as it's XML parser.  No other changes should be
+    # required to use Nokogiri as the XML parser.
+    #
+    # Example (using UW ITS Web Services):
+    #
+    #   require 'rubygems'
+    #   require 'nokogiri'
+    #   gem 'soap4r'
+    #   require 'defaultDriver'
+    #   require 'xsd/xmlparser/nokogiri'
+    #   
+    #   obj = AvlPortType.new
+    #   obj.getLatestByRoute(obj.getAgencies.first, 8).each do |bus|
+    #     p "#{bus.routeID}, #{bus.longitude}, #{bus.latitude}"
+    #   end
+    #
+    class Nokogiri < XSD::XMLParser::Parser
+      ###
+      # Create a new XSD parser with +host+ and +opt+
+      def initialize host, opt = {}
+        super
+        @parser = ::Nokogiri::XML::SAX::Parser.new(self, @charset || 'UTF-8')
+      end
+
+      ###
+      # Start parsing +string_or_readable+
+      def do_parse string_or_readable
+        @parser.parse(string_or_readable)
+      end
+
+      ###
+      # Handle the start_element event with +name+ and +attrs+
+      def start_element name, attrs = []
+        super(name, Hash[*attrs.flatten])
+      end
+
+      ###
+      # Handle the end_element event with +name+
+      def end_element name
+        super
+      end
+
+      ###
+      # Handle errors with message +msg+
+      def error msg
+        raise ParseError.new(msg)
+      end
+      alias :warning :error
+
+      ###
+      # Handle cdata_blocks containing +string+
+      def cdata_block string
+        characters string
+      end
+
+      def start_element_namespace name, attrs = [], prefix = nil, uri = nil, ns = []
+        ###
+        # Deal with SAX v1 interface
+        name = [prefix, name].compact.join(':')
+        attributes = ns.map { |ns_prefix,ns_uri|
+          [['xmlns', ns_prefix].compact.join(':'), ns_uri]
+        } + attrs.map { |attr|
+          [[attr.prefix, attr.localname].compact.join(':'), attr.value]
+        }.flatten
+        start_element name, attributes
+      end
+
+      def end_element_namespace name, prefix = nil, uri = nil
+        ###
+        # Deal with SAX v1 interface
+        end_element [prefix, name].compact.join(':')
+      end
+
+      %w{ xmldecl start_document end_document comment }.each do |name|
+        class_eval %{ def #{name}(*args); end }
+      end
+
+      add_factory(self)
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/tasks/cross_compile.rb

@@ -0,0 +1,173 @@
+require 'rake/extensioncompiler'
+HOST = Rake::ExtensionCompiler.mingw_host
+TARGET = 'i386-pc-mingw32'
+
+ZLIB    = 'zlib-1.2.5'
+ICONV   = 'libiconv-1.13.1'
+LIBXML  = 'libxml2-2.7.7'
+LIBXSLT = 'libxslt-1.1.26'
+RAKE_COMPILER_PKGCONFIG = File.expand_path(File.join(Dir.pwd, "tmp/cross/lib/pkgconfig/"))
+
+### Build zlib ###
+file "tmp/cross/download/#{ZLIB}" do |t|
+  FileUtils.mkdir_p('tmp/cross/download')
+
+  file = ZLIB
+  url  = "http://zlib.net/#{file}.tar.gz"
+
+  Dir.chdir('tmp/cross/download') do
+    sh "wget #{url} || curl -O #{url}"
+    sh "tar zxvf #{file}.tar.gz"
+  end
+
+  Dir.chdir t.name do
+    mk = File.read('win32/Makefile.gcc')
+    File.open('win32/Makefile.gcc', 'wb') do |f|
+      f.puts "BINARY_PATH = #{CROSS_DIR}/bin"
+      f.puts "LIBRARY_PATH = #{CROSS_DIR}/lib"
+      f.puts "INCLUDE_PATH = #{CROSS_DIR}/include"
+
+      f.puts mk.sub(/^PREFIX\s*=\s*$/, "PREFIX = #{HOST}-") #.
+        #sub(/^SHARED_MODE=0$/, 'SHARED_MODE=1').
+        #sub(/^IMPLIB\s*=.*$/, 'IMPLIB=libz.dll.a')
+    end
+  end
+end
+
+file 'tmp/cross/lib/libz.a' => "tmp/cross/download/#{ZLIB}" do |t|
+  Dir.chdir t.prerequisites.first do
+    sh 'make -f win32/Makefile.gcc'
+    sh 'make -f win32/Makefile.gcc install'
+  end
+end
+### End build zlib ###
+
+### Build iconv ###
+file "tmp/cross/download/#{ICONV}" do |t|
+  FileUtils.mkdir_p('tmp/cross/download')
+
+  file = ICONV
+  url  = "http://ftp.gnu.org/pub/gnu/libiconv/#{file}.tar.gz"
+
+  Dir.chdir('tmp/cross/download') do
+    sh "wget #{url} || curl -O #{url}"
+    sh "tar zxvf #{file}.tar.gz"
+  end
+
+  Dir.chdir t.name do
+    sh "./configure --disable-shared --enable-static --host=#{HOST} --target=#{TARGET} --prefix=#{CROSS_DIR} CPPFLAGS='-mno-cygwin -Wall' CFLAGS='-mno-cygwin -O2 -g' CXXFLAGS='-mno-cygwin -O2 -g' LDFLAGS=-mno-cygwin"
+  end
+end
+
+file 'tmp/cross/bin/iconv.exe' => "tmp/cross/download/#{ICONV}" do |t|
+  Dir.chdir t.prerequisites.first do
+    sh 'make'
+    sh 'make install'
+  end
+end
+### End build iconv ###
+
+### Build libxml2 ###
+file "tmp/cross/download/#{LIBXML}" do |t|
+  FileUtils.mkdir_p('tmp/cross/download')
+
+  file = LIBXML
+  url  = "ftp://ftp.xmlsoft.org/libxml2/#{file}.tar.gz"
+
+  Dir.chdir('tmp/cross/download') do
+    sh "wget #{url} || curl -O #{url}"
+    sh "tar zxvf #{file}.tar.gz"
+  end
+
+  Dir.chdir t.name do
+    sh "CFLAGS='-DIN_LIBXML' ./configure --host=#{HOST} --target=#{TARGET} --enable-static --disable-shared --prefix=#{CROSS_DIR} --with-zlib=#{CROSS_DIR} --with-iconv=#{CROSS_DIR} --without-python --without-readline"
+  end
+end
+
+file 'tmp/cross/bin/xml2-config' => "tmp/cross/download/#{LIBXML}" do |t|
+  Dir.chdir t.prerequisites.first do
+    sh 'make LDFLAGS="-avoid-version"'
+    sh 'make install'
+  end
+end
+### End build libxml2 ###
+
+### Build libxslt ###
+file "tmp/cross/download/#{LIBXSLT}" do |t|
+  FileUtils.mkdir_p('tmp/cross/download')
+
+  file = LIBXSLT
+  url  = "ftp://ftp.xmlsoft.org/libxml2/#{file}.tar.gz"
+
+  Dir.chdir('tmp/cross/download') do
+    sh "wget #{url} || curl -O #{url}"
+    sh "tar zxvf #{file}.tar.gz"
+  end
+
+  Dir.chdir t.name do
+    sh "CFLAGS='-DIN_LIBXML' ./configure --host=#{HOST} --target=#{TARGET} --enable-static --disable-shared --prefix=#{CROSS_DIR} --with-libxml-prefix=#{CROSS_DIR} --without-python --without-crypto"
+  end
+end
+
+file 'tmp/cross/bin/xslt-config' => "tmp/cross/download/#{LIBXSLT}" do |t|
+  Dir.chdir t.prerequisites.first do
+    sh 'make LDFLAGS="-avoid-version"'
+    sh 'make install'
+  end
+end
+### End build libxslt ###
+
+file 'lib/nokogiri/nokogiri.rb' => 'cross:check' do
+  File.open("lib/#{HOE.name}/#{HOE.name}.rb", 'wb') do |f|
+    f.write <<-eoruby
+require "#{HOE.name}/\#{RUBY_VERSION.sub(/\\.\\d+$/, '')}/#{HOE.name}"
+    eoruby
+  end
+end
+
+namespace :cross do
+  task :iconv   => 'tmp/cross/bin/iconv.exe'
+  task :zlib    => 'tmp/cross/lib/libz.a'
+  task :libxml2 => ['cross:zlib', 'cross:iconv', 'tmp/cross/bin/xml2-config']
+  task :libxslt => ['cross:libxml2', 'tmp/cross/bin/xslt-config']
+
+  task :check => ["cross:libxslt"] do
+    unless File.directory?(RAKE_COMPILER_PKGCONFIG)
+      raise RuntimeError.new("looks like rake-compiler changed where pkgconfig info is kept. (#{RAKE_COMPILER_PKGCONFIG})")
+    end
+  end
+
+  task :file_list do
+    HOE.spec.extensions = []
+    HOE.spec.files += Dir["lib/#{HOE.name}/#{HOE.name}.rb"]
+    HOE.spec.files += Dir["lib/#{HOE.name}/1.{8,9}/#{HOE.name}.so"]
+  end
+end
+
+CLOBBER.include("lib/nokogiri/nokogiri.{so,dylib,rb,bundle}")
+CLOBBER.include("lib/nokogiri/1.{8,9}")
+
+if Rake::Task.task_defined?(:cross)
+  Rake::Task[:cross].prerequisites << "lib/nokogiri/nokogiri.rb"
+  Rake::Task[:cross].prerequisites << "cross:file_list"
+end
+
+desc "build a windows gem without all the ceremony."
+task "gem:windows" do
+  rake_compiler_config = YAML.load_file("#{ENV['HOME']}/.rake-compiler/config.yml")
+
+  # check that rake-compiler config contains the right patchlevels of 1.8.6 and 1.9.1. see #279.
+  ["1.8.6-p383", "1.9.1-p243"].each do |version|
+    majmin, patchlevel = version.split("-")
+    rbconfig = "rbconfig-#{majmin}"
+    unless rake_compiler_config.key?(rbconfig) && rake_compiler_config[rbconfig] =~ /-#{patchlevel}/
+      raise "rake-compiler '#{rbconfig}' not #{patchlevel}. try running 'env --unset=HOST rake-compiler cross-ruby VERSION=#{version}'"
+    end
+  end
+
+  # verify that --export-all is in the 1.9.1 rbconfig. see #279,#374,#375.
+  rbconfig_191 = rake_compiler_config["rbconfig-1.9.1"]
+  raise "rbconfig #{rbconfig_191} needs --export-all in its DLDFLAGS value" if File.read(rbconfig_191).grep(/CONFIG\["DLDFLAGS"\].*--export-all/).empty?
+
+  system("env PKG_CONFIG_PATH=#{RAKE_COMPILER_PKGCONFIG} RUBY_CC_VERSION=1.8.6:1.9.1 rake cross native gem") || raise("build failed!")
+end