search_biomodel 1.0.0 → 1.0.1

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

@@ -1,164 +0,0 @@
-module Nokogiri
-  module XML
-    ###
-    # SAX Parsers are event driven parsers.  Nokogiri provides two different
-    # event based parsers when dealing with XML.  If you want to do SAX style
-    # parsing using HTML, check out Nokogiri::HTML::SAX.
-    #
-    # The basic way a SAX style parser works is by creating a parser,
-    # telling the parser about the events we're interested in, then giving
-    # the parser some XML to process.  The parser will notify you when
-    # it encounters events you said you would like to know about.
-    #
-    # To register for events, you simply subclass Nokogiri::XML::SAX::Document,
-    # and implement the methods for which you would like notification.
-    #
-    # For example, if I want to be notified when a document ends, and when an
-    # element starts, I would write a class like this:
-    #
-    #   class MyDocument < Nokogiri::XML::SAX::Document
-    #     def end_document
-    #       puts "the document has ended"
-    #     end
-    #
-    #     def start_element name, attributes = []
-    #       puts "#{name} started"
-    #     end
-    #   end
-    #
-    # Then I would instantiate a SAX parser with this document, and feed the
-    # parser some XML
-    #
-    #   # Create a new parser
-    #   parser = Nokogiri::XML::SAX::Parser.new(MyDocument.new)
-    #
-    #   # Feed the parser some XML
-    #   parser.parse(File.read(ARGV[0], 'rb'))
-    #
-    # Now my document handler will be called when each node starts, and when
-    # the document ends.  To see what kinds of events are available, take
-    # a look at Nokogiri::XML::SAX::Document.
-    #
-    # Two SAX parsers for XML are available, a parser that reads from a string
-    # or IO object as it feels necessary, and a parser that lets you spoon
-    # feed it XML.  If you want to let Nokogiri deal with reading your XML,
-    # use the Nokogiri::XML::SAX::Parser.  If you want to have fine grain
-    # control over the XML input, use the Nokogiri::XML::SAX::PushParser.
-    module SAX
-      ###
-      # This class is used for registering types of events you are interested
-      # in handling.  All of the methods on this class are available as
-      # possible events while parsing an XML document.  To register for any
-      # particular event, just subclass this class and implement the methods
-      # you are interested in knowing about.
-      #
-      # To only be notified about start and end element events, write a class
-      # like this:
-      #
-      #   class MyDocument < Nokogiri::XML::SAX::Document
-      #     def start_element name, attrs = []
-      #       puts "#{name} started!"
-      #     end
-      #
-      #     def end_element name
-      #       puts "#{name} ended"
-      #     end
-      #   end
-      #
-      # You can use this event handler for any SAX style parser included with
-      # Nokogiri.  See Nokogiri::XML::SAX, and Nokogiri::HTML::SAX.
-      class Document
-        ###
-        # Called when an XML declaration is parsed
-        def xmldecl version, encoding, standalone
-        end
-
-        ###
-        # Called when document starts parsing
-        def start_document
-        end
-
-        ###
-        # Called when document ends parsing
-        def end_document
-        end
-
-        ###
-        # Called at the beginning of an element
-        # * +name+ is the name of the tag
-        # * +attrs+ are an assoc list of namespaces and attributes, e.g.:
-        #     [ ["xmlns:foo", "http://sample.net"], ["size", "large"] ]
-        def start_element name, attrs = []
-        end
-
-        ###
-        # Called at the end of an element
-        # +name+ is the tag name
-        def end_element name
-        end
-
-        ###
-        # Called at the beginning of an element
-        # +name+ is the element name
-        # +attrs+ is a list of attributes
-        # +prefix+ is the namespace prefix for the element
-        # +uri+ is the associated namespace URI
-        # +ns+ is a hash of namespace prefix:urls associated with the element
-        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]
-          }
-          start_element name, attributes
-        end
-
-        ###
-        # Called at the end of an element
-        # +name+ is the element's name
-        # +prefix+ is the namespace prefix associated with the element
-        # +uri+ is the associated namespace URI
-        def end_element_namespace name, prefix = nil, uri = nil
-          ###
-          # Deal with SAX v1 interface
-          end_element [prefix, name].compact.join(':')
-        end
-
-        ###
-        # Characters read between a tag.  This method might be called multiple
-        # times given one contiguous string of characters.
-        #
-        # +string+ contains the character data
-        def characters string
-        end
-
-        ###
-        # Called when comments are encountered
-        # +string+ contains the comment data
-        def comment string
-        end
-
-        ###
-        # Called on document warnings
-        # +string+ contains the warning
-        def warning string
-        end
-
-        ###
-        # Called on document errors
-        # +string+ contains the error
-        def error string
-        end
-
-        ###
-        # Called when cdata blocks are found
-        # +string+ contains the cdata content
-        def cdata_block string
-        end
-      end
-    end
-  end
-end

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

@@ -1,115 +0,0 @@
-module Nokogiri
-  module XML
-    module SAX
-      ###
-      # This parser is a SAX style parser that reads it's input as it
-      # deems necessary.  The parser takes a Nokogiri::XML::SAX::Document,
-      # an optional encoding, then given an XML input, sends messages to
-      # the Nokogiri::XML::SAX::Document.
-      #
-      # Here is an example of using this parser:
-      #
-      #   # Create a subclass of Nokogiri::XML::SAX::Document and implement
-      #   # the events we care about:
-      #   class MyDoc < Nokogiri::XML::SAX::Document
-      #     def start_element name, attrs = []
-      #       puts "starting: #{name}"
-      #     end
-      #
-      #     def end_element name
-      #       puts "ending: #{name}"
-      #     end
-      #   end
-      #
-      #   # Create our parser
-      #   parser = Nokogiri::XML::SAX::Parser.new(MyDoc.new)
-      #
-      #   # Send some XML to the parser
-      #   parser.parse(File.read(ARGV[0]))
-      #
-      # For more information about SAX parsers, see Nokogiri::XML::SAX.  Also
-      # see Nokogiri::XML::SAX::Document for the available events.
-      class Parser
-        class Attribute < Struct.new(:localname, :prefix, :uri, :value)
-        end
-
-        # Encodinds this parser supports
-        ENCODINGS = {
-          'NONE'        => 0, # No char encoding detected
-          'UTF-8'       => 1, # UTF-8
-          'UTF16LE'     => 2, # UTF-16 little endian
-          'UTF16BE'     => 3, # UTF-16 big endian
-          'UCS4LE'      => 4, # UCS-4 little endian
-          'UCS4BE'      => 5, # UCS-4 big endian
-          'EBCDIC'      => 6, # EBCDIC uh!
-          'UCS4-2143'   => 7, # UCS-4 unusual ordering
-          'UCS4-3412'   => 8, # UCS-4 unusual ordering
-          'UCS2'        => 9, # UCS-2
-          'ISO-8859-1'  => 10, # ISO-8859-1 ISO Latin 1
-          'ISO-8859-2'  => 11, # ISO-8859-2 ISO Latin 2
-          'ISO-8859-3'  => 12, # ISO-8859-3
-          'ISO-8859-4'  => 13, # ISO-8859-4
-          'ISO-8859-5'  => 14, # ISO-8859-5
-          'ISO-8859-6'  => 15, # ISO-8859-6
-          'ISO-8859-7'  => 16, # ISO-8859-7
-          'ISO-8859-8'  => 17, # ISO-8859-8
-          'ISO-8859-9'  => 18, # ISO-8859-9
-          'ISO-2022-JP' => 19, # ISO-2022-JP
-          'SHIFT-JIS'   => 20, # Shift_JIS
-          'EUC-JP'      => 21, # EUC-JP
-          'ASCII'       => 22, # pure ASCII
-        }
-
-        # The Nokogiri::XML::SAX::Document where events will be sent.
-        attr_accessor :document
-
-        # The encoding beings used for this document.
-        attr_accessor :encoding
-
-        # Create a new Parser with +doc+ and +encoding+
-        def initialize doc = Nokogiri::XML::SAX::Document.new, encoding = 'UTF-8'
-          @encoding = encoding
-          @document = doc
-          @warned   = false
-        end
-
-        ###
-        # Parse given +thing+ which may be a string containing xml, or an
-        # IO object.
-        def parse thing, &block
-          if thing.respond_to?(:read) && thing.respond_to?(:close)
-            parse_io(thing, &block)
-          else
-            parse_memory(thing, &block)
-          end
-        end
-
-        ###
-        # Parse given +io+
-        def parse_io io, encoding = 'ASCII'
-          @encoding = encoding
-          ctx = ParserContext.io(io, ENCODINGS[encoding])
-          yield ctx if block_given?
-          ctx.parse_with self
-        end
-
-        ###
-        # Parse a file with +filename+
-        def parse_file filename
-          raise ArgumentError unless filename
-          raise Errno::ENOENT unless File.exists?(filename)
-          raise Errno::EISDIR if File.directory?(filename)
-          ctx = ParserContext.file filename
-          yield ctx if block_given?
-          ctx.parse_with self
-        end
-
-        def parse_memory data
-          ctx = ParserContext.memory data
-          yield ctx if block_given?
-          ctx.parse_with self
-        end
-      end
-    end
-  end
-end

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

@@ -1,16 +0,0 @@
-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

@@ -1,60 +0,0 @@
-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/sax.rb

@@ -1,4 +0,0 @@
-require 'nokogiri/xml/sax/document'
-require 'nokogiri/xml/sax/parser_context'
-require 'nokogiri/xml/sax/parser'
-require 'nokogiri/xml/sax/push_parser'

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

@@ -1,63 +0,0 @@
-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

@@ -1,47 +0,0 @@
-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

@@ -1,9 +0,0 @@
-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/syntax_error.rb

@@ -1,11 +0,0 @@
-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.rb

@@ -1,10 +0,0 @@
-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_context.rb

@@ -1,16 +0,0 @@
-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/xml.rb

@@ -1,67 +0,0 @@
-require 'nokogiri/xml/pp'
-require 'nokogiri/xml/parse_options'
-require 'nokogiri/xml/sax'
-require 'nokogiri/xml/node'
-require 'nokogiri/xml/attribute_decl'
-require 'nokogiri/xml/element_decl'
-require 'nokogiri/xml/element_content'
-require 'nokogiri/xml/character_data'
-require 'nokogiri/xml/namespace'
-require 'nokogiri/xml/attr'
-require 'nokogiri/xml/dtd'
-require 'nokogiri/xml/cdata'
-require 'nokogiri/xml/text'
-require 'nokogiri/xml/document'
-require 'nokogiri/xml/document_fragment'
-require 'nokogiri/xml/processing_instruction'
-require 'nokogiri/xml/node_set'
-require 'nokogiri/xml/syntax_error'
-require 'nokogiri/xml/xpath'
-require 'nokogiri/xml/xpath_context'
-require 'nokogiri/xml/builder'
-require 'nokogiri/xml/reader'
-require 'nokogiri/xml/notation'
-require 'nokogiri/xml/entity_decl'
-require 'nokogiri/xml/schema'
-require 'nokogiri/xml/relax_ng'
-
-module Nokogiri
-  class << self
-    ###
-    # Parse XML.  Convenience method for Nokogiri::XML::Document.parse
-    def XML thing, url = nil, encoding = nil, options = XML::ParseOptions::DEFAULT_XML, &block
-      Nokogiri::XML::Document.parse(thing, url, encoding, options, &block)
-    end
-  end
-
-  module XML
-    class << self
-      ###
-      # Parse an XML document using the Nokogiri::XML::Reader API.  See
-      # Nokogiri::XML::Reader for mor information
-      def Reader string_or_io, url = nil, encoding = nil, options = ParseOptions::STRICT
-
-        options = Nokogiri::XML::ParseOptions.new(options) if Fixnum === options
-        # Give the options to the user
-        yield options if block_given?
-
-        if string_or_io.respond_to? :read
-          return Reader.from_io(string_or_io, url, encoding, options.to_i)
-        end
-        Reader.from_memory(string_or_io, url, encoding, options.to_i)
-      end
-
-      ###
-      # Parse XML.  Convenience method for Nokogiri::XML::Document.parse
-      def parse thing, url = nil, encoding = nil, options = ParseOptions::DEFAULT_XML, &block
-        Document.parse(thing, url, encoding, options, &block)
-      end
-
-      ####
-      # Parse a fragment from +string+ in to a NodeSet.
-      def fragment string
-        XML::DocumentFragment.parse(string)
-      end
-    end
-  end
-end

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

@@ -1,25 +0,0 @@
-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/nokogiri/xslt.rb

@@ -1,52 +0,0 @@
-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