search_biomodel 1.0.0 → 1.0.1

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

@@ -1,70 +0,0 @@
-#include <xml_attribute_decl.h>
-
-/*
- * call-seq:
- *  attribute_type
- *
- * The attribute_type for this AttributeDecl
- */
-static VALUE attribute_type(VALUE self)
-{
-  xmlAttributePtr node;
-  Data_Get_Struct(self, xmlAttribute, node);
-  return INT2NUM((long)node->atype);
-}
-
-/*
- * call-seq:
- *  default
- *
- * The default value
- */
-static VALUE default_value(VALUE self)
-{
-  xmlAttributePtr node;
-  Data_Get_Struct(self, xmlAttribute, node);
-
-  if(node->defaultValue) return NOKOGIRI_STR_NEW2(node->defaultValue);
-  return Qnil;
-}
-
-/*
- * call-seq:
- *  enumeration
- *
- * An enumeration of possible values
- */
-static VALUE enumeration(VALUE self)
-{
-  xmlAttributePtr node;
-  xmlEnumerationPtr enm;
-  VALUE list;
-
-  Data_Get_Struct(self, xmlAttribute, node);
-
-  list = rb_ary_new();
-  enm = node->tree;
-
-  while(enm) {
-    rb_ary_push(list, NOKOGIRI_STR_NEW2(enm->name));
-    enm = enm->next;
-  }
-
-  return list;
-}
-
-VALUE cNokogiriXmlAttributeDecl;
-
-void init_xml_attribute_decl()
-{
-  VALUE nokogiri = rb_define_module("Nokogiri");
-  VALUE xml = rb_define_module_under(nokogiri, "XML");
-  VALUE node = rb_define_class_under(xml, "Node", rb_cObject);
-  VALUE klass = rb_define_class_under(xml, "AttributeDecl", node);
-
-  cNokogiriXmlAttributeDecl = klass;
-
-  rb_define_method(klass, "attribute_type", attribute_type, 0);
-  rb_define_method(klass, "default", default_value, 0);
-  rb_define_method(klass, "enumeration", enumeration, 0);
-}

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

@@ -1,9 +0,0 @@
-#ifndef NOKOGIRI_XML_ATTRIBUTE_DECL
-#define NOKOGIRI_XML_ATTRIBUTE_DECL
-
-#include <nokogiri.h>
-
-void init_xml_attribute_decl();
-
-extern VALUE cNokogiriXmlAttributeDecl;
-#endif

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

@@ -1,56 +0,0 @@
-#include <xml_cdata.h>
-
-/*
- * call-seq:
- *  new(document, content)
- *
- * Create a new CDATA element on the +document+ with +content+
- */
-static VALUE new(int argc, VALUE *argv, VALUE klass)
-{
-  xmlDocPtr xml_doc;
-  xmlNodePtr node;
-  VALUE doc;
-  VALUE content;
-  VALUE rest;
-  VALUE rb_node;
-
-  rb_scan_args(argc, argv, "2*", &doc, &content, &rest);
-
-  Data_Get_Struct(doc, xmlDoc, xml_doc);
-
-  node = xmlNewCDataBlock(
-      xml_doc->doc,
-      NIL_P(content) ? NULL : (const xmlChar *)StringValuePtr(content),
-      NIL_P(content) ? 0 : (int)RSTRING_LEN(content)
-  );
-
-  NOKOGIRI_ROOT_NODE(node);
-
-  rb_node = Nokogiri_wrap_xml_node(klass, node);
-  rb_obj_call_init(rb_node, argc, argv);
-
-  if(rb_block_given_p()) rb_yield(rb_node);
-
-  return rb_node;
-}
-
-VALUE cNokogiriXmlCData;
-void init_xml_cdata()
-{
-  VALUE nokogiri = rb_define_module("Nokogiri");
-  VALUE xml = rb_define_module_under(nokogiri, "XML");
-  VALUE node = rb_define_class_under(xml, "Node", rb_cObject);
-  VALUE char_data = rb_define_class_under(xml, "CharacterData", node);
-  VALUE text = rb_define_class_under(xml, "Text", char_data);
-
-  /*
-   * CData represents a CData node in an xml document.
-   */
-  VALUE klass = rb_define_class_under(xml, "CDATA", text);
-
-
-  cNokogiriXmlCData = klass;
-
-  rb_define_singleton_method(klass, "new", new, -1);
-}

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

@@ -1,9 +0,0 @@
-#ifndef NOKOGIRI_XML_CDATA
-#define NOKOGIRI_XML_CDATA
-
-#include <nokogiri.h>
-
-void init_xml_cdata();
-
-extern VALUE cNokogiriXmlCData;
-#endif

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

@@ -1,54 +0,0 @@
-#include <xml_comment.h>
-
-/*
- * call-seq:
- *  new(document, content)
- *
- * Create a new Comment element on the +document+ with +content+
- */
-static VALUE new(int argc, VALUE *argv, VALUE klass)
-{
-  xmlDocPtr xml_doc;
-  xmlNodePtr node;
-  VALUE document;
-  VALUE content;
-  VALUE rest;
-  VALUE rb_node;
-
-  rb_scan_args(argc, argv, "2*", &document, &content, &rest);
-
-  Data_Get_Struct(document, xmlDoc, xml_doc);
-
-  node = xmlNewDocComment(
-      xml_doc,
-      (const xmlChar *)StringValuePtr(content)
-  );
-
-  rb_node = Nokogiri_wrap_xml_node(klass, node);
-  rb_obj_call_init(rb_node, argc, argv);
-
-  NOKOGIRI_ROOT_NODE(node);
-
-  if(rb_block_given_p()) rb_yield(rb_node);
-
-  return rb_node;
-}
-
-VALUE cNokogiriXmlComment;
-void init_xml_comment()
-{
-  VALUE nokogiri = rb_define_module("Nokogiri");
-  VALUE xml = rb_define_module_under(nokogiri, "XML");
-  VALUE node = rb_define_class_under(xml, "Node", rb_cObject);
-  VALUE char_data = rb_define_class_under(xml, "CharacterData", node);
-
-  /*
-   * Comment represents a comment node in an xml document.
-   */
-  VALUE klass = rb_define_class_under(xml, "Comment", char_data);
-
-
-  cNokogiriXmlComment = klass;
-
-  rb_define_singleton_method(klass, "new", new, -1);
-}

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

@@ -1,9 +0,0 @@
-#ifndef NOKOGIRI_XML_COMMENT
-#define NOKOGIRI_XML_COMMENT
-
-#include <nokogiri.h>
-
-void init_xml_comment();
-
-extern VALUE cNokogiriXmlComment;
-#endif

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

@@ -1,478 +0,0 @@
-#include <xml_document.h>
-
-static int dealloc_node_i(xmlNodePtr key, xmlNodePtr node, xmlDocPtr doc)
-{
-  switch(node->type) {
-  case XML_ATTRIBUTE_NODE:
-    xmlFreePropList((xmlAttrPtr)node);
-    break;
-  case XML_NAMESPACE_DECL:
-    xmlFree(node);
-    break;
-  default:
-    if(node->parent == NULL) {
-      xmlAddChild((xmlNodePtr)doc, node);
-    }
-  }
-  return ST_CONTINUE;
-}
-
-static void dealloc(xmlDocPtr doc)
-{
-  xmlDeregisterNodeFunc func;
-  st_table *node_hash;
-
-  NOKOGIRI_DEBUG_START(doc);
-  func = xmlDeregisterNodeDefault(NULL);
-
-  node_hash  = DOC_UNLINKED_NODE_HASH(doc);
-
-  st_foreach(node_hash, dealloc_node_i, (st_data_t)doc);
-  st_free_table(node_hash);
-
-  free(doc->_private);
-  doc->_private = NULL;
-  xmlFreeDoc(doc);
-
-  xmlDeregisterNodeDefault(func);
-  NOKOGIRI_DEBUG_END(doc);
-}
-
-static void recursively_remove_namespaces_from_node(xmlNodePtr node)
-{
-  xmlNodePtr child ;
-  xmlAttrPtr property ;
-
-  xmlSetNs(node, NULL);
-
-  for (child = node->children ; child ; child = child->next)
-    recursively_remove_namespaces_from_node(child);
-
-  if (node->nsDef) {
-    xmlFreeNsList(node->nsDef);
-    node->nsDef = NULL;
-  }
-
-  if (node->properties != NULL) {
-    property = node->properties ;
-    while (property != NULL) {
-      if (property->ns) property->ns = NULL ;
-      property = property->next ;
-    }
-  }
-}
-
-/*
- * call-seq:
- *  url
- *
- * Get the url name for this document.
- */
-static VALUE url(VALUE self)
-{
-  xmlDocPtr doc;
-  Data_Get_Struct(self, xmlDoc, doc);
-
-  if(doc->URL) return NOKOGIRI_STR_NEW2(doc->URL);
-
-  return Qnil;
-}
-
-/*
- * call-seq:
- *  root=
- *
- * Set the root element on this document
- */
-static VALUE set_root(VALUE self, VALUE root)
-{
-  xmlDocPtr doc;
-  xmlNodePtr new_root;
-  xmlNodePtr old_root;
-
-  Data_Get_Struct(self, xmlDoc, doc);
-
-  old_root = NULL;
-
-  if(NIL_P(root)) {
-    old_root = xmlDocGetRootElement(doc);
-
-    if(old_root) {
-      xmlUnlinkNode(old_root);
-      NOKOGIRI_ROOT_NODE(old_root);
-    }
-
-    return root;
-  }
-
-  Data_Get_Struct(root, xmlNode, new_root);
-
-
-  /* If the new root's document is not the same as the current document,
-   * then we need to dup the node in to this document. */
-  if(new_root->doc != doc) {
-    old_root = xmlDocGetRootElement(doc);
-    if (!(new_root = xmlDocCopyNode(new_root, doc, 1))) {
-      rb_raise(rb_eRuntimeError, "Could not reparent node (xmlDocCopyNode)");
-    }
-  }
-
-  xmlDocSetRootElement(doc, new_root);
-  if(old_root) NOKOGIRI_ROOT_NODE(old_root);
-  return root;
-}
-
-/*
- * call-seq:
- *  root
- *
- * Get the root node for this document.
- */
-static VALUE root(VALUE self)
-{
-  xmlDocPtr doc;
-  xmlNodePtr root;
-
-  Data_Get_Struct(self, xmlDoc, doc);
-
-  root = xmlDocGetRootElement(doc);
-
-  if(!root) return Qnil;
-  return Nokogiri_wrap_xml_node(Qnil, root) ;
-}
-
-/*
- * call-seq:
- *  encoding= encoding
- *
- * Set the encoding string for this Document
- */
-static VALUE set_encoding(VALUE self, VALUE encoding)
-{
-  xmlDocPtr doc;
-  Data_Get_Struct(self, xmlDoc, doc);
-
-  doc->encoding = xmlStrdup((xmlChar *)StringValuePtr(encoding));
-
-  return encoding;
-}
-
-/*
- * call-seq:
- *  encoding
- *
- * Get the encoding for this Document
- */
-static VALUE encoding(VALUE self)
-{
-  xmlDocPtr doc;
-  Data_Get_Struct(self, xmlDoc, doc);
-
-  if(!doc->encoding) return Qnil;
-  return NOKOGIRI_STR_NEW2(doc->encoding);
-}
-
-/*
- * call-seq:
- *  version
- *
- * Get the XML version for this Document
- */
-static VALUE version(VALUE self)
-{
-  xmlDocPtr doc;
-  Data_Get_Struct(self, xmlDoc, doc);
-
-  if(!doc->version) return Qnil;
-  return NOKOGIRI_STR_NEW2(doc->version);
-}
-
-/*
- * call-seq:
- *  read_io(io, url, encoding, options)
- *
- * Create a new document from an IO object
- */
-static VALUE read_io( VALUE klass,
-                      VALUE io,
-                      VALUE url,
-                      VALUE encoding,
-                      VALUE options )
-{
-  const char * c_url    = NIL_P(url)      ? NULL : StringValuePtr(url);
-  const char * c_enc    = NIL_P(encoding) ? NULL : StringValuePtr(encoding);
-  VALUE error_list      = rb_ary_new();
-  VALUE document;
-  xmlDocPtr doc;
-
-  xmlResetLastError();
-  xmlSetStructuredErrorFunc((void *)error_list, Nokogiri_error_array_pusher);
-
-  doc = xmlReadIO(
-      (xmlInputReadCallback)io_read_callback,
-      (xmlInputCloseCallback)io_close_callback,
-      (void *)io,
-      c_url,
-      c_enc,
-      (int)NUM2INT(options)
-  );
-  xmlSetStructuredErrorFunc(NULL, NULL);
-
-  if(doc == NULL) {
-    xmlErrorPtr error;
-
-    xmlFreeDoc(doc);
-
-    error = xmlGetLastError();
-    if(error)
-      rb_exc_raise(Nokogiri_wrap_xml_syntax_error((VALUE)NULL, error));
-    else
-      rb_raise(rb_eRuntimeError, "Could not parse document");
-
-    return Qnil;
-  }
-
-  document = Nokogiri_wrap_xml_document(klass, doc);
-  rb_iv_set(document, "@errors", error_list);
-  return document;
-}
-
-/*
- * call-seq:
- *  read_memory(string, url, encoding, options)
- *
- * Create a new document from a String
- */
-static VALUE read_memory( VALUE klass,
-                          VALUE string,
-                          VALUE url,
-                          VALUE encoding,
-                          VALUE options )
-{
-  const char * c_buffer = StringValuePtr(string);
-  const char * c_url    = NIL_P(url)      ? NULL : StringValuePtr(url);
-  const char * c_enc    = NIL_P(encoding) ? NULL : StringValuePtr(encoding);
-  int len               = (int)RSTRING_LEN(string);
-  VALUE error_list      = rb_ary_new();
-  VALUE document;
-  xmlDocPtr doc;
-
-  xmlResetLastError();
-  xmlSetStructuredErrorFunc((void *)error_list, Nokogiri_error_array_pusher);
-  doc = xmlReadMemory(c_buffer, len, c_url, c_enc, (int)NUM2INT(options));
-  xmlSetStructuredErrorFunc(NULL, NULL);
-
-  if(doc == NULL) {
-    xmlErrorPtr error;
-
-    xmlFreeDoc(doc);
-
-    error = xmlGetLastError();
-    if(error)
-      rb_exc_raise(Nokogiri_wrap_xml_syntax_error((VALUE)NULL, error));
-    else
-      rb_raise(rb_eRuntimeError, "Could not parse document");
-
-    return Qnil;
-  }
-
-  document = Nokogiri_wrap_xml_document(klass, doc);
-  rb_iv_set(document, "@errors", error_list);
-  return document;
-}
-
-/*
- * call-seq:
- *  dup
- *
- * Copy this Document.  An optional depth may be passed in, but it defaults
- * to a deep copy.  0 is a shallow copy, 1 is a deep copy.
- */
-static VALUE duplicate_node(int argc, VALUE *argv, VALUE self)
-{
-  xmlDocPtr doc, dup;
-  VALUE level;
-
-  if(rb_scan_args(argc, argv, "01", &level) == 0)
-    level = INT2NUM((long)1);
-
-  Data_Get_Struct(self, xmlDoc, doc);
-
-  dup = xmlCopyDoc(doc, (int)NUM2INT(level));
-  if(dup == NULL) return Qnil;
-
-  dup->type = doc->type;
-  return Nokogiri_wrap_xml_document(rb_obj_class(self), dup);
-}
-
-/*
- * call-seq:
- *  new(version = default)
- *
- * Create a new document with +version+ (defaults to "1.0")
- */
-static VALUE new(int argc, VALUE *argv, VALUE klass)
-{
-  xmlDocPtr doc;
-  VALUE version, rest, rb_doc ;
-
-  rb_scan_args(argc, argv, "0*", &rest);
-  version = rb_ary_entry(rest, (long)0);
-  if (NIL_P(version)) version = rb_str_new2("1.0");
-
-  doc = xmlNewDoc((xmlChar *)StringValuePtr(version));
-  rb_doc = Nokogiri_wrap_xml_document(klass, doc);
-  rb_obj_call_init(rb_doc, argc, argv);
-  return rb_doc ;
-}
-
-/*
- *  call-seq:
- *    remove_namespaces!
- *
- *  Remove all namespaces from all nodes in the document.
- *
- *  This could be useful for developers who either don't understand namespaces
- *  or don't care about them.
- *
- *  The following example shows a use case, and you can decide for yourself
- *  whether this is a good thing or not:
- *
- *    doc = Nokogiri::XML <<-EOXML
- *       <root>
- *         <car xmlns:part="http://general-motors.com/">
- *           <part:tire>Michelin Model XGV</part:tire>
- *         </car>
- *         <bicycle xmlns:part="http://schwinn.com/">
- *           <part:tire>I'm a bicycle tire!</part:tire>
- *         </bicycle>
- *       </root>
- *       EOXML
- *    
- *    doc.xpath("//tire").to_s # => ""
- *    doc.xpath("//part:tire", "part" => "http://general-motors.com/").to_s # => "<part:tire>Michelin Model XGV</part:tire>"
- *    doc.xpath("//part:tire", "part" => "http://schwinn.com/").to_s # => "<part:tire>I'm a bicycle tire!</part:tire>"
- *    
- *    doc.remove_namespaces!
- *    
- *    doc.xpath("//tire").to_s # => "<tire>Michelin Model XGV</tire><tire>I'm a bicycle tire!</tire>"
- *    doc.xpath("//part:tire", "part" => "http://general-motors.com/").to_s # => ""
- *    doc.xpath("//part:tire", "part" => "http://schwinn.com/").to_s # => ""
- *
- *  For more information on why this probably is *not* a good thing in general,
- *  please direct your browser to
- *  http://tenderlovemaking.com/2009/04/23/namespaces-in-xml/
- */
-VALUE remove_namespaces_bang(VALUE self)
-{
-  xmlDocPtr doc ;
-  Data_Get_Struct(self, xmlDoc, doc);
-
-  recursively_remove_namespaces_from_node((xmlNodePtr)doc);
-  return self;
-}
-
-/* call-seq: doc.create_entity(name, type, external_id, system_id, content)
- *
- * Create a new entity named +name+.
- *
- * +type+ is an integer representing the type of entity to be created, and it
- * defaults to Nokogiri::XML::EntityDecl::INTERNAL_GENERAL.  See
- * the constants on Nokogiri::XML::EntityDecl for more information.
- *
- * +external_id+, +system_id+, and +content+ set the External ID, System ID,
- * and content respectively.  All of these parameters are optional.
- */
-static VALUE create_entity(int argc, VALUE *argv, VALUE self)
-{
-  VALUE name;
-  VALUE type;
-  VALUE external_id;
-  VALUE system_id;
-  VALUE content;
-  xmlEntityPtr ptr;
-  xmlDocPtr doc ;
-
-  Data_Get_Struct(self, xmlDoc, doc);
-
-  rb_scan_args(argc, argv, "14", &name, &type, &external_id, &system_id,
-      &content);
-
-  xmlResetLastError();
-  ptr = xmlAddDocEntity(
-      doc,
-      (xmlChar *)(NIL_P(name)        ? NULL                        : StringValuePtr(name)),
-      (int)      (NIL_P(type)        ? XML_INTERNAL_GENERAL_ENTITY : NUM2INT(type)),
-      (xmlChar *)(NIL_P(external_id) ? NULL                        : StringValuePtr(external_id)),
-      (xmlChar *)(NIL_P(system_id)   ? NULL                        : StringValuePtr(system_id)),
-      (xmlChar *)(NIL_P(content)     ? NULL                        : StringValuePtr(content))
-    );
-
-  if(NULL == ptr) {
-    xmlErrorPtr error = xmlGetLastError();
-    if(error)
-      rb_exc_raise(Nokogiri_wrap_xml_syntax_error((VALUE)NULL, error));
-    else
-      rb_raise(rb_eRuntimeError, "Could not create entity");
-
-    return Qnil;
-  }
-
-  return Nokogiri_wrap_xml_node(cNokogiriXmlEntityDecl, (xmlNodePtr)ptr);
-}
-
-VALUE cNokogiriXmlDocument ;
-void init_xml_document()
-{
-  VALUE nokogiri  = rb_define_module("Nokogiri");
-  VALUE xml       = rb_define_module_under(nokogiri, "XML");
-  VALUE node      = rb_define_class_under(xml, "Node", rb_cObject);
-
-  /*
-   * Nokogiri::XML::Document wraps an xml document.
-   */
-  VALUE klass = rb_define_class_under(xml, "Document", node);
-
-  cNokogiriXmlDocument = klass;
-
-  rb_define_singleton_method(klass, "read_memory", read_memory, 4);
-  rb_define_singleton_method(klass, "read_io", read_io, 4);
-  rb_define_singleton_method(klass, "new", new, -1);
-
-  rb_define_method(klass, "root", root, 0);
-  rb_define_method(klass, "root=", set_root, 1);
-  rb_define_method(klass, "encoding", encoding, 0);
-  rb_define_method(klass, "encoding=", set_encoding, 1);
-  rb_define_method(klass, "version", version, 0);
-  rb_define_method(klass, "dup", duplicate_node, -1);
-  rb_define_method(klass, "url", url, 0);
-  rb_define_method(klass, "create_entity", create_entity, -1);
-  rb_define_method(klass, "remove_namespaces!", remove_namespaces_bang, 0);
-}
-
-
-/* this takes klass as a param because it's used for HtmlDocument, too. */
-VALUE Nokogiri_wrap_xml_document(VALUE klass, xmlDocPtr doc)
-{
-  nokogiriTuplePtr tuple = (nokogiriTuplePtr)malloc(sizeof(nokogiriTuple));
-
-  VALUE rb_doc = Data_Wrap_Struct(
-      klass ? klass : cNokogiriXmlDocument,
-      0,
-      dealloc,
-      doc
-  );
-
-  VALUE cache = rb_ary_new();
-  rb_iv_set(rb_doc, "@decorators", Qnil);
-  rb_iv_set(rb_doc, "@node_cache", cache);
-
-  tuple->doc = (void *)rb_doc;
-  tuple->unlinkedNodes = st_init_numtable_with_size(128);
-  tuple->node_cache = cache;
-  doc->_private = tuple ;
-
-  rb_obj_call_init(rb_doc, 0, NULL);
-
-  return rb_doc ;
-}