search_biomodel 0.1.2 → 1.0.0

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

@@ -0,0 +1,43 @@
+# :stopdoc:
+module Nokogiri
+  module XML
+    class ElementContent
+      attr_accessor :cstruct
+
+      def self.wrap pointer, document
+        return nil if pointer.null?
+
+        c = ElementContent.allocate
+        c.cstruct = LibXML::XmlElementContent.new pointer
+        c.instance_variable_set :@document, document
+        c
+      end
+
+      def type
+        cstruct[:type]
+      end
+
+      def prefix
+        cstruct[:prefix]
+      end
+
+      def occur
+        cstruct[:ocur]
+      end
+
+      def name
+        cstruct[:name]
+      end
+
+      private
+      def c1
+        self.class.wrap cstruct[:c1], document
+      end
+
+      def c2
+        self.class.wrap cstruct[:c2], document
+      end
+    end
+  end
+end
+# :startdoc:

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

@@ -0,0 +1,19 @@
+# :stopdoc:
+module Nokogiri
+  module XML
+    class ElementDecl < Nokogiri::XML::Node
+      def element_type
+        cstruct[:etype]
+      end
+
+      def prefix
+        cstruct[:prefix]
+      end
+
+      def content
+        ElementContent.wrap cstruct[:content], document
+      end
+    end
+  end
+end
+# :startdoc:

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

@@ -0,0 +1,36 @@
+# :stopdoc:
+module Nokogiri
+  module XML
+    class EntityDecl < Nokogiri::XML::Node
+
+      # from libxml/entities.h
+      INTERNAL_GENERAL          = 1
+      EXTERNAL_GENERAL_PARSED   = 2
+      EXTERNAL_GENERAL_UNPARSED = 3
+      INTERNAL_PARAMETER        = 4
+      EXTERNAL_PARAMETER        = 5
+      INTERNAL_PREDEFINED       = 6
+
+      def content
+        cstruct[:content]
+      end
+
+      def entity_type
+        cstruct[:etype]
+      end
+
+      def external_id
+        cstruct[:external_id]
+      end
+
+      def system_id
+        cstruct[:system_id]
+      end
+
+      def original_content
+        cstruct[:orig]
+      end
+    end
+  end
+end
+# :startdoc:

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

@@ -0,0 +1,19 @@
+module Nokogiri
+  module XML
+    class EntityReference < Node
+
+      def self.new(document, name, *rest) # :nodoc:
+        node_ptr = LibXML.xmlNewReference(document.cstruct, name)
+        node_cstruct = LibXML::XmlNode.new(node_ptr)
+        node_cstruct.keep_reference_from_document!
+
+        node = Node.wrap(node_cstruct, self)
+        node.send :initialize, document, name, *rest
+        yield node if block_given?
+        node
+      end
+
+    end
+  end
+end
+

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

@@ -0,0 +1,44 @@
+module Nokogiri
+  module XML
+    class Namespace
+      # :stopdoc:
+
+      attr_accessor :cstruct
+      attr_accessor :document
+
+      def prefix
+        cstruct[:prefix].nil? ? nil : cstruct[:prefix] # TODO: encoding?
+      end
+
+      def href
+        cstruct[:href].nil? ? nil : cstruct[:href] # TODO: encoding?
+      end
+
+      class << self
+        def wrap(document, node_struct)
+          if node_struct.is_a?(FFI::Pointer)
+            # cast native pointers up into a node cstruct
+            return nil if node_struct.null?
+            node_struct = LibXML::XmlNs.new(node_struct) 
+          end
+
+          ruby_node = node_struct.ruby_node
+          return ruby_node unless ruby_node.nil?
+
+          ns = Nokogiri::XML::Namespace.allocate
+          ns.document = document.ruby_doc
+          ns.cstruct = node_struct
+
+          ns.cstruct.ruby_node = ns
+
+          cache = ns.document.instance_variable_get(:@node_cache)
+          cache << ns
+
+          ns
+        end
+      end
+
+      # :startdoc:
+    end
+  end
+end

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

@@ -0,0 +1,559 @@
+module Nokogiri
+  module XML
+    class Node
+      # :stopdoc:
+
+      attr_accessor :cstruct
+
+      def pointer_id
+        cstruct.pointer
+      end
+
+      def encode_special_chars(string)
+        char_ptr = LibXML.xmlEncodeSpecialChars(self[:doc], string)
+        encoded = char_ptr.read_string
+        # TODO: encoding?
+        LibXML.xmlFree(char_ptr)
+        encoded
+      end
+
+      def internal_subset
+        doc = cstruct.document
+        dtd = LibXML.xmlGetIntSubset(doc)
+        return nil if dtd.null?
+        Node.wrap(dtd)
+      end
+
+      def external_subset
+        doc = cstruct.document
+        return nil if doc[:extSubset].null?
+
+        Node.wrap(doc[:extSubset])
+      end
+
+      def create_internal_subset name, external_id, system_id
+        raise("Document already has an internal subset") if internal_subset
+
+        doc = cstruct.document
+        dtd_ptr = LibXML.xmlCreateIntSubset doc, name, external_id, system_id
+
+        return nil if dtd_ptr.null?
+
+        Node.wrap dtd_ptr
+      end
+
+      def create_external_subset name, external_id, system_id
+        raise("Document already has an external subset") if external_subset
+
+        doc = cstruct.document
+        dtd_ptr = LibXML.xmlNewDtd doc, name, external_id, system_id
+
+        return nil if dtd_ptr.null?
+
+        Node.wrap dtd_ptr
+      end
+
+      def dup(deep = 1)
+        dup_ptr = LibXML.xmlDocCopyNode(cstruct, cstruct.document, deep)
+        return nil if dup_ptr.null?
+        Node.wrap(dup_ptr, self.class)
+      end
+
+      def unlink
+        LibXML.xmlUnlinkNode(cstruct)
+        cstruct.keep_reference_from_document!
+        self
+      end
+
+      def blank?
+        LibXML.xmlIsBlankNode(cstruct) == 1
+      end
+
+      def next_sibling
+        cstruct_node_from :next
+      end
+
+      def previous_sibling
+        cstruct_node_from :prev
+      end
+
+      def next_element
+        LibXML.xmlNextElementSiblingHack self
+      end
+
+      def previous_element
+        #
+        #  note that we don't use xmlPreviousElementSibling here because it's buggy pre-2.7.7.
+        #
+        sibling_ptr = cstruct[:prev]
+
+        while ! sibling_ptr.null?
+          sibling_cstruct = LibXML::XmlNode.new(sibling_ptr)
+          break if sibling_cstruct[:type] == ELEMENT_NODE
+          sibling_ptr = sibling_cstruct[:prev]
+        end
+
+        return sibling_ptr.null? ? nil : Node.wrap(sibling_ptr)
+      end
+
+      def replace_node new_node
+        Node.reparent_node_with(self, new_node) do |pivot_struct, reparentee_struct|
+          retval = LibXML.xmlReplaceNode(pivot_struct, reparentee_struct)
+          retval = reparentee_struct if retval == pivot_struct.pointer # for reparent_node_with semantics
+          retval = LibXML::XmlNode.new(retval) if retval.is_a?(FFI::Pointer)
+          if retval[:type] == TEXT_NODE
+            if !retval[:prev].null? && LibXML::XmlNode.new(retval[:prev])[:type] == TEXT_NODE
+              retval = LibXML::XmlNode.new(LibXML.xmlTextMerge(retval[:prev], retval))
+            end
+            if !retval[:next].null? && LibXML::XmlNode.new(retval[:next])[:type] == TEXT_NODE
+              retval = LibXML::XmlNode.new(LibXML.xmlTextMerge(retval, retval[:next]))
+            end
+          end
+          retval
+        end
+      end
+
+      def children
+        return NodeSet.new(nil) if cstruct[:children].null?
+        child = Node.wrap(cstruct[:children])
+
+        set = NodeSet.wrap(LibXML.xmlXPathNodeSetCreate(child.cstruct), self.document)
+        return set unless child
+
+        child_ptr = child.cstruct[:next]
+        while ! child_ptr.null?
+          child = Node.wrap(child_ptr)
+          LibXML.xmlXPathNodeSetAddUnique(set.cstruct, child.cstruct)
+          child_ptr = child.cstruct[:next]
+        end
+
+        return set
+      end
+
+      def element_children
+        child = LibXML.xmlFirstElementChildHack(self)
+        return NodeSet.new(nil) if child.nil?
+
+        set = NodeSet.wrap(LibXML.xmlXPathNodeSetCreate(child.cstruct), self.document)
+        return set unless child
+
+        next_sibling = LibXML.xmlNextElementSiblingHack(child)
+        while ! next_sibling.nil?
+          child = next_sibling
+          LibXML.xmlXPathNodeSetAddUnique(set.cstruct, child.cstruct)
+          next_sibling = LibXML.xmlNextElementSiblingHack(child)
+        end
+
+        return set
+      end
+
+      def child
+        (val = cstruct[:children]).null? ? nil : Node.wrap(val)
+      end
+
+      def first_element_child
+        LibXML.xmlFirstElementChildHack(self)
+      end
+
+      def last_element_child
+        LibXML.xmlLastElementChildHack(self)
+      end
+
+      def key?(attribute)
+        ! (prop = LibXML.xmlHasProp(cstruct, attribute.to_s)).null?
+      end
+
+      def namespaced_key?(attribute, namespace)
+        prop = LibXML.xmlHasNsProp(cstruct, attribute.to_s,
+          namespace.nil? ? nil : namespace.to_s)
+        !prop.null?
+      end
+
+      def []=(property, value)
+        LibXML.xmlSetProp(cstruct, property, value)
+        value
+      end
+
+      def get(attribute)
+        return nil unless attribute
+        propstr = LibXML.xmlGetProp(cstruct, attribute.to_s)
+        return nil if propstr.null?
+        rval = propstr.read_string # TODO: encoding?
+        LibXML.xmlFree(propstr)
+        rval
+      end
+
+      def set_namespace(namespace)
+        LibXML.xmlSetNs(cstruct, namespace ? namespace.cstruct : nil)
+        self
+      end
+
+      def attribute(name)
+        attribute_nodes.find { |x| x.name == name }
+      end
+
+      def attribute_with_ns(name, namespace)
+        prop = LibXML.xmlHasNsProp(cstruct, name.to_s,
+          namespace.nil? ? NULL : namespace.to_s)
+        return prop if prop.null?
+        Node.wrap(prop)
+      end
+
+      def attribute_nodes
+        Node.node_properties cstruct
+      end
+
+      def namespace
+        cstruct[:ns].null? ? nil : Namespace.wrap(cstruct.document, cstruct[:ns])
+      end
+
+      def namespace_definitions
+        list = []
+        ns_ptr = cstruct[:nsDef]
+        return list if ns_ptr.null?
+        while ! ns_ptr.null?
+          ns = Namespace.wrap(cstruct.document, ns_ptr)
+          list << ns
+          ns_ptr = ns.cstruct[:next]
+        end
+        list
+      end
+
+      def namespace_scopes
+        ns_list = LibXML.xmlGetNsList(self.cstruct[:doc], self.cstruct)
+        return [] if ns_list.null?
+
+        list = []
+        until (ns_ptr = ns_list.get_pointer(LibXML.pointer_offset(list.length))).null?
+          list << Namespace.wrap(cstruct.document, ns_ptr)
+        end
+
+        LibXML.xmlFree(ns_list)
+        list
+      end
+
+      def node_type
+        cstruct[:type]
+      end
+
+      def native_content=(content)
+        child_ptr = cstruct[:children]
+        while ! child_ptr.null?
+          child    = Node.wrap(child_ptr)
+          next_ptr = child.cstruct[:next]
+          LibXML.xmlUnlinkNode(child.cstruct)
+          cstruct.keep_reference_from_document!
+          child_ptr = next_ptr
+        end
+        LibXML.xmlNodeSetContent(cstruct, content)
+        content
+      end
+
+      def content
+        content_ptr = LibXML.xmlNodeGetContent(cstruct)
+        return nil if content_ptr.null?
+        content = content_ptr.read_string # TODO: encoding?
+        LibXML.xmlFree(content_ptr)
+        content
+      end
+
+      def add_child_node child
+        Node.reparent_node_with(self, child) do |pivot_struct, reparentee_struct|
+          LibXML.xmlAddChild(pivot_struct, reparentee_struct)
+        end
+      end
+
+      def parent
+        cstruct_node_from :parent
+      end
+
+      def node_name=(string)
+        LibXML.xmlNodeSetName(cstruct, string)
+        string
+      end
+
+      def node_name
+        cstruct[:name] # TODO: encoding?
+      end
+
+      def path
+        path_ptr = LibXML.xmlGetNodePath(cstruct)
+        val = path_ptr.null? ? nil : path_ptr.read_string # TODO: encoding?
+        LibXML.xmlFree(path_ptr)
+        val
+      end
+
+      def add_next_sibling_node next_sibling
+        Node.reparent_node_with(self, next_sibling) do |pivot_struct, reparentee_struct|
+          LibXML.xmlAddNextSibling(pivot_struct, reparentee_struct)
+        end
+      end
+
+      def add_previous_sibling_node prev_sibling
+        Node.reparent_node_with(self, prev_sibling) do |pivot_struct, reparentee_struct|
+          LibXML.xmlAddPrevSibling(pivot_struct, reparentee_struct)
+        end
+      end
+
+      def native_write_to(io, encoding, indent_string, options)
+        set_xml_indent_tree_output 1
+        set_xml_tree_indent_string indent_string
+        savectx = LibXML.xmlSaveToIO(IoCallbacks.writer(io), nil, nil, encoding, options)
+        LibXML.xmlSaveTree(savectx, cstruct)
+        LibXML.xmlSaveClose(savectx)
+        io
+      end
+
+      def line
+        cstruct[:line]
+      end
+
+      def add_namespace_definition(prefix, href)
+        ns = LibXML.xmlSearchNs(cstruct.document, cstruct, prefix.nil? ? nil : prefix.to_s)
+        namespacee = self
+        if ns.null?
+          namespacee = parent if type != ELEMENT_NODE
+          ns = LibXML.xmlNewNs(namespacee.cstruct, href, prefix)
+        end
+        return nil if ns.null?
+        LibXML.xmlSetNs(cstruct, ns) if (prefix.nil? || self != namespacee)
+        Namespace.wrap(cstruct.document, ns)
+      end
+
+      def self.new(name, doc, *rest)
+        ptr = LibXML.xmlNewNode(nil, name.to_s)
+
+        node_cstruct = LibXML::XmlNode.new(ptr)
+        node_cstruct[:doc] = doc.cstruct[:doc]
+        node_cstruct.keep_reference_from_document!
+
+        node = Node.wrap(
+          node_cstruct,
+          Node == self ? nil : self
+        )
+        node.send :initialize, name, doc, *rest
+        yield node if block_given?
+        node
+      end
+
+      def dump_html
+        return to_xml if type == DOCUMENT_NODE
+        buffer = LibXML::XmlBuffer.new(LibXML.xmlBufferCreate())
+        LibXML.htmlNodeDump(buffer, cstruct[:doc], cstruct)
+        buffer[:content] # TODO: encoding?
+      end
+
+      def compare(other)
+        LibXML.xmlXPathCmpNodes(other.cstruct, self.cstruct)
+      end
+
+      def self.wrap(node_struct, klass=nil)
+        if node_struct.is_a?(FFI::Pointer)
+          # cast native pointers up into a node cstruct
+          return nil if node_struct.null?
+          node_struct = LibXML::XmlNode.new(node_struct)
+        end
+
+        raise "wrapping a node without a document" unless node_struct.document
+
+        document_struct = node_struct.document
+        document_obj = document_struct.nil? ? nil : document_struct.ruby_doc
+        if node_struct[:type] == DOCUMENT_NODE || node_struct[:type] == HTML_DOCUMENT_NODE
+          return document_obj
+        end
+
+        ruby_node = node_struct.ruby_node
+        return ruby_node unless ruby_node.nil?
+
+        klasses = case node_struct[:type]
+                  when ELEMENT_NODE then [XML::Element]
+                  when TEXT_NODE then [XML::Text]
+                  when ENTITY_REF_NODE then [XML::EntityReference]
+                  when ATTRIBUTE_DECL then [XML::AttributeDecl, LibXML::XmlAttribute]
+                  when ELEMENT_DECL then [XML::ElementDecl, LibXML::XmlElement]
+                  when COMMENT_NODE then [XML::Comment]
+                  when DOCUMENT_FRAG_NODE then [XML::DocumentFragment]
+                  when PI_NODE then [XML::ProcessingInstruction]
+                  when ATTRIBUTE_NODE then [XML::Attr]
+                  when ENTITY_DECL then [XML::EntityDecl, LibXML::XmlEntity]
+                  when CDATA_SECTION_NODE then [XML::CDATA]
+                  when DTD_NODE then [XML::DTD, LibXML::XmlDtd]
+                  else [XML::Node]
+                  end
+
+        if klass
+          node = klass.allocate
+        else
+          node = klasses.first.allocate
+        end
+        node.cstruct = klasses[1] ? klasses[1].new(node_struct.pointer) : node_struct
+
+        node.cstruct.ruby_node = node
+
+        if document_obj
+          node.instance_variable_set(:@document, document_obj)
+          cache = document_obj.instance_variable_get(:@node_cache)
+          cache << node
+          document_obj.decorate(node)
+        end
+
+        node
+      end
+
+      def document
+        cstruct.document.ruby_doc
+      end
+
+      def in_context(string, options)
+        errors = []
+        LibXML.xmlSetStructuredErrorFunc(nil, SyntaxError.error_array_pusher(errors))
+        LibXML.htmlHandleOmittedElem(0)
+
+        list_memory = FFI::MemoryPointer.new :pointer
+        LibXML.xmlParseInNodeContext(cstruct, string, string.length, options, list_memory)
+
+        self.document.children.each do |child|
+          if child.cstruct[:parent] != cstruct[:doc]
+            child.cstruct[:parent] = cstruct[:doc]
+          end
+        end
+
+        LibXML.htmlHandleOmittedElem(1)
+        LibXML.xmlSetStructuredErrorFunc(nil, nil)
+        self.document.errors = errors
+
+        set = NodeSet.wrap(LibXML.xmlXPathNodeSetCreate(nil), document)
+        list_ptr = list_memory.get_pointer(0)
+        while ! list_ptr.null?
+          list = Node.wrap(list_ptr)
+          LibXML.xmlXPathNodeSetAddUnique(set.cstruct, list.cstruct)
+          list_ptr = list.cstruct[:next]
+        end
+        set
+      end
+
+      class << self
+        def node_properties(cstruct)
+          attr = []
+          prop_cstruct = cstruct[:properties]
+          while ! prop_cstruct.null?
+            prop = Node.wrap(prop_cstruct)
+            attr << prop
+            prop_cstruct = prop.cstruct[:next]
+          end
+          attr
+        end
+      end
+
+      private
+
+      def self.reparent_node_with(pivot, reparentee, &block)
+        raise(ArgumentError, "node must be a Nokogiri::XML::Node") unless reparentee.is_a?(Nokogiri::XML::Node)
+        raise(ArgumentError, "cannot reparent a document node") if reparentee.node_type == DOCUMENT_NODE || reparentee.node_type == HTML_DOCUMENT_NODE
+
+        pivot_struct = pivot.cstruct
+        reparentee_struct = reparentee.cstruct
+
+        LibXML.xmlUnlinkNode(reparentee_struct)
+
+        if reparentee_struct[:doc] != pivot_struct[:doc] || reparentee_struct[:type] == TEXT_NODE
+          reparentee_struct.keep_reference_from_document!
+          reparentee_struct = LibXML.xmlDocCopyNode(reparentee_struct, pivot_struct.document, 1)
+          raise(RuntimeError, "Could not reparent node (xmlDocCopyNode)") unless reparentee_struct
+          reparentee_struct = LibXML::XmlNode.new(reparentee_struct)
+        end
+
+        if reparentee_struct[:type] == TEXT_NODE && !pivot_struct[:next].null?
+          next_text = Node.wrap(pivot_struct[:next])
+          if next_text.cstruct[:type] == TEXT_NODE
+            new_next_text = LibXML.xmlDocCopyNode(next_text.cstruct, pivot_struct[:doc], 1)
+            LibXML.xmlUnlinkNode(next_text.cstruct)
+            next_text.cstruct.keep_reference_from_document!
+            LibXML.xmlAddNextSibling(pivot_struct, new_next_text);
+          end
+        end
+
+        if reparentee_struct[:type] == TEXT_NODE && pivot_struct[:type] == TEXT_NODE && Nokogiri.is_2_6_16?
+          pivot_struct.pointer.put_pointer(pivot_struct.offset_of(:content), LibXML.xmlStrdup(pivot_struct[:content]))
+        end
+
+        reparented_struct = block.call(pivot_struct, reparentee_struct)
+        raise(RuntimeError, "Could not reparent node") unless reparented_struct
+
+        reparented_struct = LibXML::XmlNode.new(reparented_struct) if reparented_struct.is_a?(FFI::Pointer)
+        reparentee.cstruct = reparented_struct
+
+        relink_namespace reparented_struct
+
+        reparented = Node.wrap(reparented_struct)
+        reparented.decorate!
+        reparented
+      end
+
+      def self.relink_namespace(reparented_struct)
+        return if reparented_struct[:parent].null?
+
+        # Make sure that our reparented node has the correct namespaces
+        if reparented_struct[:ns].null? && reparented_struct[:doc] != reparented_struct[:parent]
+          LibXML.xmlSetNs(reparented_struct, LibXML::XmlNode.new(reparented_struct[:parent])[:ns])
+        end
+
+        # Search our parents for an existing definition
+        if ! reparented_struct[:nsDef].null?
+          curr = reparented_struct[:nsDef]
+          prev = nil
+
+          while (! curr.null?)
+            curr_ns = LibXML::XmlNs.new(curr)
+            ns = LibXML.xmlSearchNsByHref(
+              reparented_struct[:doc],
+              reparented_struct[:parent],
+              curr_ns[:href]
+              )
+            # If we find the namespace is already declared, remove it from this
+            # definition list.
+            if (! ns.null? && ns != curr)
+              if prev
+                prev[:next] = curr_ns[:next]
+              else
+                reparented_struct[:nsDef] = curr_ns[:next]
+              end
+              curr_ns.keep_reference_from!(reparented_struct.document)
+            else
+              prev = curr_ns
+            end
+            curr = curr_ns[:next]
+          end
+        end
+
+        # Only walk all children if there actually is a namespace we need to reparent.
+        return if reparented_struct[:ns].null?
+
+        # When a node gets reparented, walk it's children to make sure that
+        # their namespaces are reparented as well.
+        child_ptr = reparented_struct[:children]
+        while ! child_ptr.null?
+          child_struct = LibXML::XmlNode.new(child_ptr)
+          relink_namespace child_struct
+          child_ptr = child_struct[:next]
+        end
+      end
+
+      def cstruct_node_from(sym)
+        (val = cstruct[sym]).null? ? nil : Node.wrap(val)
+      end
+
+      def set_xml_indent_tree_output(value)
+        LibXML.__xmlIndentTreeOutput.write_int(value)
+      end
+
+      def set_xml_tree_indent_string(value)
+        LibXML.__xmlTreeIndentString.write_pointer(LibXML.xmlStrdup(value.to_s))
+      end
+
+      # :startdoc:
+    end
+  end
+end
+class Nokogiri::XML::Element < Nokogiri::XML::Node; end
+class Nokogiri::XML::CharacterData < Nokogiri::XML::Node; end