search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_processing_instruction.h

@@ -0,0 +1,9 @@
+#ifndef NOKOGIRI_XML_PROCESSING_INSTRUCTION
+#define NOKOGIRI_XML_PROCESSING_INSTRUCTION
+
+#include <nokogiri.h>
+
+void init_xml_processing_instruction();
+
+extern VALUE cNokogiriXmlProcessingInstruction;
+#endif

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_reader.c

@@ -0,0 +1,684 @@
+#include <xml_reader.h>
+
+static void dealloc(xmlTextReaderPtr reader)
+{
+  NOKOGIRI_DEBUG_START(reader);
+  xmlFreeTextReader(reader);
+  NOKOGIRI_DEBUG_END(reader);
+}
+
+static int has_attributes(xmlTextReaderPtr reader)
+{
+  /*
+   *  this implementation of xmlTextReaderHasAttributes explicitly includes
+   *  namespaces and properties, because some earlier versions ignore
+   *  namespaces.
+   */
+  xmlNodePtr node ;
+  node = xmlTextReaderCurrentNode(reader);
+  if (node == NULL)
+    return(0);
+
+  if ((node->type == XML_ELEMENT_NODE) &&
+      ((node->properties != NULL) || (node->nsDef != NULL)))
+    return(1);
+  return(0);
+}
+
+#define XMLNS_PREFIX "xmlns"
+#define XMLNS_PREFIX_LEN 6 /* including either colon or \0 */
+#define XMLNS_BUFFER_LEN 128
+static void Nokogiri_xml_node_namespaces(xmlNodePtr node, VALUE attr_hash)
+{
+  xmlNsPtr ns;
+  static char buffer[XMLNS_BUFFER_LEN] ;
+  char *key ;
+  size_t keylen ;
+
+  if (node->type != XML_ELEMENT_NODE) return ;
+
+  ns = node->nsDef;
+  while (ns != NULL) {
+
+    keylen = XMLNS_PREFIX_LEN + (ns->prefix ? (strlen((const char*)ns->prefix) + 1) : 0) ;
+    if (keylen > XMLNS_BUFFER_LEN) {
+      key = (char*)malloc(keylen) ;
+    } else {
+      key = buffer ;
+    }
+
+    if (ns->prefix) {
+      sprintf(key, "%s:%s", XMLNS_PREFIX, ns->prefix);
+    } else {
+      sprintf(key, "%s", XMLNS_PREFIX);
+    }
+
+    rb_hash_aset(attr_hash,
+        NOKOGIRI_STR_NEW2(key),
+        (ns->href ? NOKOGIRI_STR_NEW2(ns->href) : Qnil)
+    );
+    if (key != buffer) {
+      free(key);
+    }
+    ns = ns->next ;
+  }
+}
+
+
+/*
+ * call-seq:
+ *   default?
+ *
+ * Was an attribute generated from the default value in the DTD or schema?
+ */
+static VALUE default_eh(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  int eh;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  eh = xmlTextReaderIsDefault(reader);
+  if(eh == 0) return Qfalse;
+  if(eh == 1) return Qtrue;
+
+  return Qnil;
+}
+
+/*
+ * call-seq:
+ *   value?
+ *
+ * Does this node have a text value?
+ */
+static VALUE value_eh(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  int eh;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  eh = xmlTextReaderHasValue(reader);
+  if(eh == 0) return Qfalse;
+  if(eh == 1) return Qtrue;
+
+  return Qnil;
+}
+
+/*
+ * call-seq:
+ *   attributes?
+ *
+ * Does this node have attributes?
+ */
+static VALUE attributes_eh(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  int eh;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  eh = has_attributes(reader);
+  if(eh == 0) return Qfalse;
+  if(eh == 1) return Qtrue;
+
+  return Qnil;
+}
+
+/*
+ * call-seq:
+ *   namespaces
+ *
+ * Get a hash of namespaces for this Node
+ */
+static VALUE namespaces(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  xmlNodePtr ptr;
+  VALUE attr ;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+
+  attr = rb_hash_new() ;
+
+  if (! has_attributes(reader))
+    return attr ;
+
+  ptr = xmlTextReaderExpand(reader);
+  if(ptr == NULL) return Qnil;
+
+  Nokogiri_xml_node_namespaces(ptr, attr);
+
+  return attr ;
+}
+
+/*
+ * call-seq:
+ *   attribute_nodes
+ *
+ * Get a list of attributes for this Node
+ */
+static VALUE attribute_nodes(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  xmlNodePtr ptr;
+  VALUE attr ;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+
+  attr = rb_ary_new() ;
+
+  if (! has_attributes(reader))
+    return attr ;
+
+  ptr = xmlTextReaderExpand(reader);
+  if(ptr == NULL) return Qnil;
+
+  Nokogiri_xml_node_properties(ptr, attr);
+
+  return attr ;
+}
+
+/*
+ * call-seq:
+ *   attribute_at(index)
+ *
+ * Get the value of attribute at +index+
+ */
+static VALUE attribute_at(VALUE self, VALUE index)
+{
+  xmlTextReaderPtr reader;
+  xmlChar *value;
+  VALUE rb_value;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+
+  if(NIL_P(index)) return Qnil;
+  index = rb_Integer(index);
+
+  value = xmlTextReaderGetAttributeNo(
+      reader,
+      (int)NUM2INT(index)
+  );
+  if(value == NULL) return Qnil;
+
+  rb_value = NOKOGIRI_STR_NEW2(value);
+  xmlFree(value);
+  return rb_value;
+}
+
+/*
+ * call-seq:
+ *   attribute(name)
+ *
+ * Get the value of attribute named +name+
+ */
+static VALUE reader_attribute(VALUE self, VALUE name)
+{
+  xmlTextReaderPtr reader;
+  xmlChar *value ;
+  VALUE rb_value;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+
+  if(NIL_P(name)) return Qnil;
+  name = StringValue(name) ;
+
+  value = xmlTextReaderGetAttribute(reader, (xmlChar*)StringValuePtr(name));
+  if(value == NULL) {
+    /* this section is an attempt to workaround older versions of libxml that
+       don't handle namespaces properly in all attribute-and-friends functions */
+    xmlChar *prefix = NULL ;
+    xmlChar *localname = xmlSplitQName2((xmlChar*)StringValuePtr(name), &prefix);
+    if (localname != NULL) {
+      value = xmlTextReaderLookupNamespace(reader, localname);
+      xmlFree(localname) ;
+    } else {
+      value = xmlTextReaderLookupNamespace(reader, prefix);
+    }
+    xmlFree(prefix);
+  }
+  if(value == NULL) return Qnil;
+
+  rb_value = NOKOGIRI_STR_NEW2(value);
+  xmlFree(value);
+  return rb_value;
+}
+
+/*
+ * call-seq:
+ *   attribute_count
+ *
+ * Get the number of attributes for the current node
+ */
+static VALUE attribute_count(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  int count;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  count = xmlTextReaderAttributeCount(reader);
+  if(count == -1) return Qnil;
+
+  return INT2NUM((long)count);
+}
+
+/*
+ * call-seq:
+ *   depth
+ *
+ * Get the depth of the node
+ */
+static VALUE depth(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  int depth;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  depth = xmlTextReaderDepth(reader);
+  if(depth == -1) return Qnil;
+
+  return INT2NUM((long)depth);
+}
+
+/*
+ * call-seq:
+ *   xml_version
+ *
+ * Get the XML version of the document being read
+ */
+static VALUE xml_version(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  const char *version;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  version = (const char *)xmlTextReaderConstXmlVersion(reader);
+  if(version == NULL) return Qnil;
+
+  return NOKOGIRI_STR_NEW2(version);
+}
+
+/*
+ * call-seq:
+ *   lang
+ *
+ * Get the xml:lang scope within which the node resides.
+ */
+static VALUE lang(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  const char *lang;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  lang = (const char *)xmlTextReaderConstXmlLang(reader);
+  if(lang == NULL) return Qnil;
+
+  return NOKOGIRI_STR_NEW2(lang);
+}
+
+/*
+ * call-seq:
+ *   value
+ *
+ * Get the text value of the node if present. Returns a utf-8 encoded string.
+ */
+static VALUE value(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  const char *value;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  value = (const char *)xmlTextReaderConstValue(reader);
+  if(value == NULL) return Qnil;
+
+  return NOKOGIRI_STR_NEW2(value);
+}
+
+/*
+ * call-seq:
+ *   prefix
+ *
+ * Get the shorthand reference to the namespace associated with the node.
+ */
+static VALUE prefix(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  const char *prefix;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  prefix = (const char *)xmlTextReaderConstPrefix(reader);
+  if(prefix == NULL) return Qnil;
+
+  return NOKOGIRI_STR_NEW2(prefix);
+}
+
+/*
+ * call-seq:
+ *   namespace_uri
+ *
+ * Get the URI defining the namespace associated with the node
+ */
+static VALUE namespace_uri(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  const char *uri;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  uri = (const char *)xmlTextReaderConstNamespaceUri(reader);
+  if(uri == NULL) return Qnil;
+
+  return NOKOGIRI_STR_NEW2(uri);
+}
+
+/*
+ * call-seq:
+ *   local_name
+ *
+ * Get the local name of the node
+ */
+static VALUE local_name(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  const char *name;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  name = (const char *)xmlTextReaderConstLocalName(reader);
+  if(name == NULL) return Qnil;
+
+  return NOKOGIRI_STR_NEW2(name);
+}
+
+/*
+ * call-seq:
+ *   name
+ *
+ * Get the name of the node. Returns a utf-8 encoded string.
+ */
+static VALUE name(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  const char *name;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  name = (const char *)xmlTextReaderConstName(reader);
+  if(name == NULL) return Qnil;
+
+  return NOKOGIRI_STR_NEW2(name);
+}
+
+/*
+ * call-seq:
+ * base_uri
+ *
+ * Get the xml:base of the node
+ */
+static VALUE base_uri(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  const char * base_uri;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+  base_uri = (const char *)xmlTextReaderBaseUri(reader);
+  if (base_uri == NULL) return Qnil;
+
+  return NOKOGIRI_STR_NEW2(base_uri);
+}
+
+/*
+ * call-seq:
+ *   state
+ *
+ * Get the state of the reader
+ */
+static VALUE state(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  Data_Get_Struct(self, xmlTextReader, reader);
+  return INT2NUM((long)xmlTextReaderReadState(reader));
+}
+
+/*
+ * call-seq:
+ *   node_type
+ *
+ * Get the type of readers current node
+ */
+static VALUE node_type(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  Data_Get_Struct(self, xmlTextReader, reader);
+  return INT2NUM((long)xmlTextReaderNodeType(reader));
+}
+
+/*
+ * call-seq:
+ *   read
+ *
+ * Move the Reader forward through the XML document.
+ */
+static VALUE read_more(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  xmlErrorPtr error;
+  VALUE error_list;
+  int ret;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+
+  error_list = rb_funcall(self, rb_intern("errors"), 0);
+
+  xmlSetStructuredErrorFunc((void *)error_list, Nokogiri_error_array_pusher);
+  ret = xmlTextReaderRead(reader);
+  xmlSetStructuredErrorFunc(NULL, NULL);
+
+  if(ret == 1) return self;
+  if(ret == 0) return Qnil;
+
+  error = xmlGetLastError();
+  if(error)
+    rb_exc_raise(Nokogiri_wrap_xml_syntax_error((VALUE)NULL, error));
+  else
+    rb_raise(rb_eRuntimeError, "Error pulling: %d", ret);
+
+  return Qnil;
+}
+
+/*
+ * call-seq:
+ *   inner_xml
+ *
+ * Read the contents of the current node, including child nodes and markup.
+ * Returns a utf-8 encoded string.
+ */
+static VALUE inner_xml(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  xmlChar* value;
+  VALUE str;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+
+  value = xmlTextReaderReadInnerXml(reader);
+
+  str = Qnil;
+  if(value) {
+    str = NOKOGIRI_STR_NEW2((char*)value);
+    xmlFree(value);
+  }
+
+  return str;
+}
+
+/*
+ * call-seq:
+ *   outer_xml
+ *
+ * Read the current node and its contents, including child nodes and markup.
+ * Returns a utf-8 encoded string.
+ */
+static VALUE outer_xml(VALUE self)
+{
+  xmlTextReaderPtr reader;
+  xmlChar *value;
+  VALUE str = Qnil;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+
+  value = xmlTextReaderReadOuterXml(reader);
+
+  if(value) {
+    str = NOKOGIRI_STR_NEW2((char*)value);
+    xmlFree(value);
+  }
+  return str;
+}
+
+/*
+ * call-seq:
+ *   from_memory(string, url = nil, encoding = nil, options = 0)
+ *
+ * Create a new reader that parses +string+
+ */
+static VALUE from_memory(int argc, VALUE *argv, VALUE klass)
+{
+  VALUE rb_buffer, rb_url, encoding, rb_options;
+  xmlTextReaderPtr reader;
+  const char * c_url      = NULL;
+  const char * c_encoding = NULL;
+  int c_options           = 0;
+  VALUE rb_reader, args[3];
+
+  rb_scan_args(argc, argv, "13", &rb_buffer, &rb_url, &encoding, &rb_options);
+
+  if (!RTEST(rb_buffer)) rb_raise(rb_eArgError, "string cannot be nil");
+  if (RTEST(rb_url)) c_url = StringValuePtr(rb_url);
+  if (RTEST(encoding)) c_encoding = StringValuePtr(encoding);
+  if (RTEST(rb_options)) c_options = (int)NUM2INT(rb_options);
+
+  reader = xmlReaderForMemory(
+      StringValuePtr(rb_buffer),
+      (int)RSTRING_LEN(rb_buffer),
+      c_url,
+      c_encoding,
+      c_options
+  );
+
+  if(reader == NULL) {
+    xmlFreeTextReader(reader);
+    rb_raise(rb_eRuntimeError, "couldn't create a parser");
+  }
+
+  rb_reader = Data_Wrap_Struct(klass, NULL, dealloc, reader);
+  args[0] = rb_buffer;
+  args[1] = rb_url;
+  args[2] = encoding;
+  rb_obj_call_init(rb_reader, 3, args);
+
+  return rb_reader;
+}
+
+/*
+ * call-seq:
+ *   from_io(io, url = nil, encoding = nil, options = 0)
+ *
+ * Create a new reader that parses +io+
+ */
+static VALUE from_io(int argc, VALUE *argv, VALUE klass)
+{
+  VALUE rb_io, rb_url, encoding, rb_options;
+  xmlTextReaderPtr reader;
+  const char * c_url      = NULL;
+  const char * c_encoding = NULL;
+  int c_options           = 0;
+  VALUE rb_reader, args[3];
+
+  rb_scan_args(argc, argv, "13", &rb_io, &rb_url, &encoding, &rb_options);
+
+  if (!RTEST(rb_io)) rb_raise(rb_eArgError, "io cannot be nil");
+  if (RTEST(rb_url)) c_url = StringValuePtr(rb_url);
+  if (RTEST(encoding)) c_encoding = StringValuePtr(encoding);
+  if (RTEST(rb_options)) c_options = (int)NUM2INT(rb_options);
+
+  reader = xmlReaderForIO(
+      (xmlInputReadCallback)io_read_callback,
+      (xmlInputCloseCallback)io_close_callback,
+      (void *)rb_io,
+      c_url,
+      c_encoding,
+      c_options
+  );
+
+  if(reader == NULL) {
+    xmlFreeTextReader(reader);
+    rb_raise(rb_eRuntimeError, "couldn't create a parser");
+  }
+
+  rb_reader = Data_Wrap_Struct(klass, NULL, dealloc, reader);
+  args[0] = rb_io;
+  args[1] = rb_url;
+  args[2] = encoding;
+  rb_obj_call_init(rb_reader, 3, args);
+
+  return rb_reader;
+}
+
+/*
+ * call-seq:
+ *   reader.empty_element? # => true or false
+ *
+ * Returns true if the current node is empty, otherwise false.
+ */
+static VALUE empty_element_p(VALUE self)
+{
+  xmlTextReaderPtr reader;
+
+  Data_Get_Struct(self, xmlTextReader, reader);
+
+  if(xmlTextReaderIsEmptyElement(reader))
+    return Qtrue;
+
+  return Qfalse;
+}
+
+VALUE cNokogiriXmlReader;
+
+void init_xml_reader()
+{
+  VALUE module = rb_define_module("Nokogiri");
+  VALUE xml = rb_define_module_under(module, "XML");
+
+  /*
+   * The Reader parser allows you to effectively pull parse an XML document.
+   * Once instantiated, call Nokogiri::XML::Reader#each to iterate over each
+   * node.  Note that you may only iterate over the document once!
+   */
+  VALUE klass = rb_define_class_under(xml, "Reader", rb_cObject);
+
+  cNokogiriXmlReader = klass;
+
+  rb_define_singleton_method(klass, "from_memory", from_memory, -1);
+  rb_define_singleton_method(klass, "from_io", from_io, -1);
+
+  rb_define_method(klass, "read", read_more, 0);
+  rb_define_method(klass, "inner_xml", inner_xml, 0);
+  rb_define_method(klass, "outer_xml", outer_xml, 0);
+  rb_define_method(klass, "state", state, 0);
+  rb_define_method(klass, "node_type", node_type, 0);
+  rb_define_method(klass, "name", name, 0);
+  rb_define_method(klass, "local_name", local_name, 0);
+  rb_define_method(klass, "namespace_uri", namespace_uri, 0);
+  rb_define_method(klass, "prefix", prefix, 0);
+  rb_define_method(klass, "value", value, 0);
+  rb_define_method(klass, "lang", lang, 0);
+  rb_define_method(klass, "xml_version", xml_version, 0);
+  rb_define_method(klass, "depth", depth, 0);
+  rb_define_method(klass, "attribute_count", attribute_count, 0);
+  rb_define_method(klass, "attribute", reader_attribute, 1);
+  rb_define_method(klass, "namespaces", namespaces, 0);
+  rb_define_method(klass, "attribute_at", attribute_at, 1);
+  rb_define_method(klass, "empty_element?", empty_element_p, 0);
+  rb_define_method(klass, "attributes?", attributes_eh, 0);
+  rb_define_method(klass, "value?", value_eh, 0);
+  rb_define_method(klass, "default?", default_eh, 0);
+  rb_define_method(klass, "base_uri", base_uri, 0);
+
+  rb_define_private_method(klass, "attr_nodes", attribute_nodes, 0);
+}