search_biomodel 1.0.0 → 1.0.1

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

@@ -1,309 +0,0 @@
-#include <xml_xpath_context.h>
-
-int vasprintf (char **strp, const char *fmt, va_list ap);
-
-static void deallocate(xmlXPathContextPtr ctx)
-{
-  NOKOGIRI_DEBUG_START(ctx);
-  xmlXPathFreeContext(ctx);
-  NOKOGIRI_DEBUG_END(ctx);
-}
-
-/*
- * call-seq:
- *  register_ns(prefix, uri)
- *
- * Register the namespace with +prefix+ and +uri+.
- */
-static VALUE register_ns(VALUE self, VALUE prefix, VALUE uri)
-{
-  xmlXPathContextPtr ctx;
-  Data_Get_Struct(self, xmlXPathContext, ctx);
-
-  xmlXPathRegisterNs( ctx,
-                      (const xmlChar *)StringValuePtr(prefix),
-                      (const xmlChar *)StringValuePtr(uri)
-  );
-  return self;
-}
-
-/*
- * call-seq:
- *  register_variable(name, value)
- *
- * Register the variable +name+ with +value+.
- */
-static VALUE register_variable(VALUE self, VALUE name, VALUE value)
-{
-   xmlXPathContextPtr ctx;
-   xmlXPathObjectPtr xmlValue;
-   Data_Get_Struct(self, xmlXPathContext, ctx);
-
-   xmlValue = xmlXPathNewCString(StringValuePtr(value));
-
-   xmlXPathRegisterVariable( ctx,
-      (const xmlChar *)StringValuePtr(name),
-      xmlValue
-   );
-
-   return self;
-}
-
-static void ruby_funcall(xmlXPathParserContextPtr ctx, int nargs)
-{
-  VALUE xpath_handler = Qnil;
-  VALUE result;
-  VALUE *argv;
-  VALUE doc;
-  VALUE node_set = Qnil;
-  xmlNodeSetPtr xml_node_set = NULL;
-  xmlXPathObjectPtr obj;
-  int i;
-
-  assert(ctx);
-  assert(ctx->context);
-  assert(ctx->context->userData);
-  assert(ctx->context->doc);
-  assert(DOC_RUBY_OBJECT_TEST(ctx->context->doc));
-
-  xpath_handler = (VALUE)(ctx->context->userData);
-
-  argv = (VALUE *)calloc((size_t)nargs, sizeof(VALUE));
-  for (i = 0 ; i < nargs ; ++i) {
-    rb_gc_register_address(&argv[i]);
-  }
-
-  doc = DOC_RUBY_OBJECT(ctx->context->doc);
-
-  i = nargs - 1;
-  do {
-    obj = valuePop(ctx);
-    switch(obj->type) {
-      case XPATH_STRING:
-        argv[i] = NOKOGIRI_STR_NEW2(obj->stringval);
-        break;
-      case XPATH_BOOLEAN:
-        argv[i] = obj->boolval == 1 ? Qtrue : Qfalse;
-        break;
-      case XPATH_NUMBER:
-        argv[i] = rb_float_new(obj->floatval);
-        break;
-      case XPATH_NODESET:
-        argv[i] = Nokogiri_wrap_xml_node_set(obj->nodesetval, doc);
-        break;
-      default:
-        argv[i] = NOKOGIRI_STR_NEW2(xmlXPathCastToString(obj));
-    }
-    xmlXPathFreeNodeSetList(obj);
-  } while(i-- > 0);
-
-  result = rb_funcall2(
-      xpath_handler,
-      rb_intern((const char *)ctx->context->function),
-      nargs,
-      argv
-  );
-
-  for (i = 0 ; i < nargs ; ++i) {
-    rb_gc_unregister_address(&argv[i]);
-  }
-  free(argv);
-
-  switch(TYPE(result)) {
-    case T_FLOAT:
-    case T_BIGNUM:
-    case T_FIXNUM:
-      xmlXPathReturnNumber(ctx, NUM2DBL(result));
-      break;
-    case T_STRING:
-      xmlXPathReturnString(
-          ctx,
-          (xmlChar *)xmlXPathWrapCString(StringValuePtr(result))
-      );
-      break;
-    case T_TRUE:
-      xmlXPathReturnTrue(ctx);
-      break;
-    case T_FALSE:
-      xmlXPathReturnFalse(ctx);
-      break;
-    case T_NIL:
-      break;
-    case T_ARRAY:
-      {
-        VALUE args[2];
-	args[0] = doc;
-	args[1] = result;
-        node_set = rb_class_new_instance(2, args, cNokogiriXmlNodeSet);
-        Data_Get_Struct(node_set, xmlNodeSet, xml_node_set);
-        xmlXPathReturnNodeSet(ctx, xmlXPathNodeSetMerge(NULL, xml_node_set));
-      }
-      break;
-    case T_DATA:
-      if(rb_obj_is_kind_of(result, cNokogiriXmlNodeSet)) {
-        Data_Get_Struct(result, xmlNodeSet, xml_node_set);
-        /* Copy the node set, otherwise it will get GC'd. */
-        xmlXPathReturnNodeSet(ctx, xmlXPathNodeSetMerge(NULL, xml_node_set));
-        break;
-      }
-    default:
-      rb_raise(rb_eRuntimeError, "Invalid return type");
-  }
-}
-
-static xmlXPathFunction lookup( void *ctx,
-                                const xmlChar * name,
-                                const xmlChar* ns_uri )
-{
-  VALUE xpath_handler = (VALUE)ctx;
-  if(rb_respond_to(xpath_handler, rb_intern((const char *)name)))
-    return ruby_funcall;
-
-  return NULL;
-}
-
-NORETURN(static void xpath_exception_handler(void * ctx, xmlErrorPtr error));
-static void xpath_exception_handler(void * ctx, xmlErrorPtr error)
-{
-  VALUE xpath = rb_const_get(mNokogiriXml, rb_intern("XPath"));
-  VALUE klass = rb_const_get(xpath, rb_intern("SyntaxError"));
-
-  rb_exc_raise(Nokogiri_wrap_xml_syntax_error(klass, error));
-}
-
-NORETURN(static void xpath_generic_exception_handler(void * ctx, const char *msg, ...));
-static void xpath_generic_exception_handler(void * ctx, const char *msg, ...)
-{
-  char * message;
-
-  va_list args;
-  va_start(args, msg);
-  vasprintf(&message, msg, args);
-  va_end(args);
-
-  rb_raise(rb_eRuntimeError, message);
-}
-
-/*
- * call-seq:
- *  evaluate(search_path, handler = nil)
- *
- * Evaluate the +search_path+ returning an XML::XPath object.
- */
-static VALUE evaluate(int argc, VALUE *argv, VALUE self)
-{
-  VALUE search_path, xpath_handler;
-  VALUE thing = Qnil;
-  xmlXPathContextPtr ctx;
-  xmlXPathObjectPtr xpath;
-  xmlChar *query;
-
-  Data_Get_Struct(self, xmlXPathContext, ctx);
-
-  if(rb_scan_args(argc, argv, "11", &search_path, &xpath_handler) == 1)
-    xpath_handler = Qnil;
-
-  query = (xmlChar *)StringValuePtr(search_path);
-
-  if(Qnil != xpath_handler) {
-    /* FIXME: not sure if this is the correct place to shove private data. */
-    ctx->userData = (void *)xpath_handler;
-    xmlXPathRegisterFuncLookup(ctx, lookup, (void *)xpath_handler);
-  }
-
-  xmlResetLastError();
-  xmlSetStructuredErrorFunc(NULL, xpath_exception_handler);
-
-  /* For some reason, xmlXPathEvalExpression will blow up with a generic error */
-  /* when there is a non existent function. */
-  xmlSetGenericErrorFunc(NULL, xpath_generic_exception_handler);
-
-  xpath = xmlXPathEvalExpression(query, ctx);
-  xmlSetStructuredErrorFunc(NULL, NULL);
-  xmlSetGenericErrorFunc(NULL, NULL);
-
-  if(xpath == NULL) {
-    VALUE xpath = rb_const_get(mNokogiriXml, rb_intern("XPath"));
-    VALUE klass = rb_const_get(xpath, rb_intern("SyntaxError"));
-
-    xmlErrorPtr error = xmlGetLastError();
-    rb_exc_raise(Nokogiri_wrap_xml_syntax_error(klass, error));
-  }
-
-  assert(ctx->doc);
-  assert(DOC_RUBY_OBJECT_TEST(ctx->doc));
-
-  switch(xpath->type) {
-    case XPATH_STRING:
-      thing = NOKOGIRI_STR_NEW2(xpath->stringval);
-      break;
-    case XPATH_NODESET:
-      if(NULL == xpath->nodesetval) {
-        thing = Nokogiri_wrap_xml_node_set(xmlXPathNodeSetCreate(NULL),
-          DOC_RUBY_OBJECT(ctx->doc));
-      } else {
-        thing = Nokogiri_wrap_xml_node_set(xpath->nodesetval,
-            DOC_RUBY_OBJECT(ctx->doc));
-      }
-      break;
-    case XPATH_NUMBER:
-      thing = rb_float_new(xpath->floatval);
-      break;
-    case XPATH_BOOLEAN:
-      thing = xpath->boolval == 1 ? Qtrue : Qfalse;
-      break;
-    default:
-      thing = Nokogiri_wrap_xml_node_set(xmlXPathNodeSetCreate(NULL),
-        DOC_RUBY_OBJECT(ctx->doc));
-  }
-
-  xmlXPathFreeNodeSetList(xpath);
-
-  return thing;
-}
-
-/*
- * call-seq:
- *  new(node)
- *
- * Create a new XPathContext with +node+ as the reference point.
- */
-static VALUE new(VALUE klass, VALUE nodeobj)
-{
-  xmlNodePtr node;
-  xmlXPathContextPtr ctx;
-  VALUE self;
-
-  xmlXPathInit();
-
-  Data_Get_Struct(nodeobj, xmlNode, node);
-
-  ctx = xmlXPathNewContext(node->doc);
-  ctx->node = node;
-  self = Data_Wrap_Struct(klass, 0, deallocate, ctx);
-  /*rb_iv_set(self, "@xpath_handler", Qnil); */
-  return self;
-}
-
-VALUE cNokogiriXmlXpathContext;
-void init_xml_xpath_context(void)
-{
-  VALUE module = rb_define_module("Nokogiri");
-
-  /*
-   * Nokogiri::XML
-   */
-  VALUE xml = rb_define_module_under(module, "XML");
-
-  /*
-   * XPathContext is the entry point for searching a Document by using XPath.
-   */
-  VALUE klass = rb_define_class_under(xml, "XPathContext", rb_cObject);
-
-  cNokogiriXmlXpathContext = klass;
-
-  rb_define_singleton_method(klass, "new", new, 1);
-  rb_define_method(klass, "evaluate", evaluate, -1);
-  rb_define_method(klass, "register_variable", register_variable, 2);
-  rb_define_method(klass, "register_ns", register_ns, 2);
-}

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

@@ -1,9 +0,0 @@
-#ifndef NOKOGIRI_XML_XPATH_CONTEXT
-#define NOKOGIRI_XML_XPATH_CONTEXT
-
-#include <nokogiri.h>
-
-void init_xml_xpath_context();
-
-extern VALUE cNokogiriXmlXpathContext;
-#endif

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

@@ -1,260 +0,0 @@
-#include <xslt_stylesheet.h>
-
-#include <libxslt/xsltInternals.h>
-#include <libxslt/xsltutils.h>
-#include <libxslt/transform.h>
-#include <libexslt/exslt.h>
-
-VALUE xslt;
-
-int vasprintf (char **strp, const char *fmt, va_list ap);
-
-static void dealloc(xsltStylesheetPtr doc)
-{
-    NOKOGIRI_DEBUG_START(doc);
-    xsltFreeStylesheet(doc); /* commented out for now. */
-    NOKOGIRI_DEBUG_END(doc);
-}
-
-NORETURN(static void xslt_generic_error_handler(void * ctx, const char *msg, ...));
-static void xslt_generic_error_handler(void * ctx, const char *msg, ...)
-{
-  char * message;
-
-  va_list args;
-  va_start(args, msg);
-  vasprintf(&message, msg, args);
-  va_end(args);
-
-  rb_exc_raise(rb_exc_new2(rb_eRuntimeError, message));
-}
-
-/*
- * call-seq:
- *   parse_stylesheet_doc(document)
- *
- * Parse a stylesheet from +document+.
- */
-static VALUE parse_stylesheet_doc(VALUE klass, VALUE xmldocobj)
-{
-    xmlDocPtr xml ;
-    xsltStylesheetPtr ss ;
-    Data_Get_Struct(xmldocobj, xmlDoc, xml);
-    exsltRegisterAll();
-
-    xsltSetGenericErrorFunc(NULL, xslt_generic_error_handler);
-
-    ss = xsltParseStylesheetDoc(xmlCopyDoc(xml, 1)); /* 1 => recursive */
-
-    xsltSetGenericErrorFunc(NULL, NULL);
-
-    return Data_Wrap_Struct(klass, NULL, dealloc, ss);
-}
-
-
-/*
- * call-seq:
- *   serialize(document)
- *
- * Serialize +document+ to an xml string.
- */
-static VALUE serialize(VALUE self, VALUE xmlobj)
-{
-    xmlDocPtr xml ;
-    xsltStylesheetPtr ss ;
-    xmlChar* doc_ptr ;
-    int doc_len ;
-    VALUE rval ;
-
-    Data_Get_Struct(xmlobj, xmlDoc, xml);
-    Data_Get_Struct(self, xsltStylesheet, ss);
-    xsltSaveResultToString(&doc_ptr, &doc_len, xml, ss);
-    rval = NOKOGIRI_STR_NEW(doc_ptr, doc_len);
-    xmlFree(doc_ptr);
-    return rval ;
-}
-
-/*
- *  call-seq:
- *    transform(document, params = [])
- *
- *  Apply an XSLT stylesheet to an XML::Document.
- *  +params+ is an array of strings used as XSLT parameters.
- *  returns Nokogiri::XML::Document
- *
- *  Example:
- * 
- *    doc   = Nokogiri::XML(File.read(ARGV[0]))
- *    xslt  = Nokogiri::XSLT(File.read(ARGV[1]))
- *    puts xslt.transform(doc, ['key', 'value'])
- *
- */
-static VALUE transform(int argc, VALUE* argv, VALUE self)
-{
-    VALUE xmldoc, paramobj ;
-    xmlDocPtr xml ;
-    xmlDocPtr result ;
-    xsltStylesheetPtr ss ;
-    const char** params ;
-    long param_len, j ;
-
-    rb_scan_args(argc, argv, "11", &xmldoc, &paramobj);
-    if (NIL_P(paramobj)) { paramobj = rb_ary_new2(0L) ; }
-    if (!rb_obj_is_kind_of(xmldoc, cNokogiriXmlDocument))
-      rb_raise(rb_eArgError, "argument must be a Nokogiri::XML::Document");
-
-    /* handle hashes as arguments. */
-    if(T_HASH == TYPE(paramobj)) {
-      paramobj = rb_funcall(paramobj, rb_intern("to_a"), 0);
-      paramobj = rb_funcall(paramobj, rb_intern("flatten"), 0);
-    }
-
-    Check_Type(paramobj, T_ARRAY);
-
-    Data_Get_Struct(xmldoc, xmlDoc, xml);
-    Data_Get_Struct(self, xsltStylesheet, ss);
-
-    param_len = RARRAY_LEN(paramobj);
-    params = calloc((size_t)param_len+1, sizeof(char*));
-    for (j = 0 ; j < param_len ; j++) {
-      VALUE entry = rb_ary_entry(paramobj, j);
-      const char * ptr = StringValuePtr(entry);
-      params[j] = ptr;
-    }
-    params[param_len] = 0 ;
-
-    result = xsltApplyStylesheet(ss, xml, params);
-    free(params);
-
-    if (!result) rb_raise(rb_eRuntimeError, "could not perform xslt transform on document");
-
-    return Nokogiri_wrap_xml_document((VALUE)0, result) ;
-}
-
-static void method_caller(xmlXPathParserContextPtr ctxt, int nargs)
-{
-    const xmlChar * function;
-    const xmlChar * functionURI;
-    size_t i, count;
-
-    xsltTransformContextPtr transform;
-    xmlXPathObjectPtr xpath;
-    VALUE obj;
-    VALUE *args;
-    VALUE result;
-
-    transform = xsltXPathGetTransformContext(ctxt);
-
-    function = ctxt->context->function;
-    functionURI = ctxt->context->functionURI;
-    obj = (VALUE)xsltGetExtData(transform, functionURI);
-
-    count = (size_t)ctxt->valueNr;
-    args = calloc(count, sizeof(VALUE *));
-
-    for(i = 0; i < count; i++) {
-	VALUE thing;
-
-	xpath = valuePop(ctxt);
-	switch(xpath->type) {
-	    case XPATH_STRING:
-		thing = NOKOGIRI_STR_NEW2(xpath->stringval);
-		break;
-	    case XPATH_NODESET:
-		if(NULL == xpath->nodesetval) {
-		    thing = Nokogiri_wrap_xml_node_set(
-			    xmlXPathNodeSetCreate(NULL),
-			    DOC_RUBY_OBJECT(ctxt->context->doc));
-		} else {
-		    thing = Nokogiri_wrap_xml_node_set(xpath->nodesetval,
-			    DOC_RUBY_OBJECT(ctxt->context->doc));
-		}
-		break;
-	    default:
-		rb_raise(rb_eRuntimeError, "do not handle type: %d", xpath->type);
-	}
-	args[i] = thing;
-    }
-    result = rb_funcall3(obj, rb_intern((const char *)function), (int)count, args);
-    switch(TYPE(result)) {
-	case T_FLOAT:
-	case T_BIGNUM:
-	case T_FIXNUM:
-	    xmlXPathReturnNumber(ctxt, NUM2DBL(result));
-	    break;
-	case T_STRING:
-	    xmlXPathReturnString(
-		    ctxt,
-		    xmlStrdup((xmlChar *)StringValuePtr(result))
-		    );
-	    break;
-	case T_TRUE:
-	    xmlXPathReturnTrue(ctxt);
-	    break;
-	case T_FALSE:
-	    xmlXPathReturnFalse(ctxt);
-	    break;
-	case T_NIL:
-	    break;
-	default:
-	    rb_raise(rb_eRuntimeError, "Invalid return type");
-    }
-}
-
-static void * initFunc(xsltTransformContextPtr ctxt, const xmlChar *uri)
-{
-    VALUE modules = rb_iv_get(xslt, "@modules");
-    VALUE obj = rb_hash_aref(modules, rb_str_new2((const char *)uri));
-    VALUE args = { Qfalse };
-    VALUE methods = rb_funcall(obj, rb_intern("instance_methods"), 1, args);
-    int i;
-
-    for(i = 0; i < RARRAY_LEN(methods); i++) {
-	VALUE method_name = rb_obj_as_string(RARRAY_PTR(methods)[i]);
-	xsltRegisterExtFunction(ctxt,
-          (unsigned char *)StringValuePtr(method_name), uri, method_caller);
-    }
-
-    return (void *)rb_class_new_instance(0, NULL, obj);
-}
-
-static void shutdownFunc(xsltTransformContextPtr ctxt,
-	const xmlChar *uri, void *data)
-{
-}
-
-/*
- *  call-seq:
- *    register(uri, custom_handler_class)
- *
- *  Register a class that implements custom XLST transformation functions.
- */
-static VALUE registr(VALUE self, VALUE uri, VALUE obj)
-{
-    VALUE modules = rb_iv_get(self, "@modules");
-    if(NIL_P(modules)) rb_raise(rb_eRuntimeError, "wtf! @modules isn't set");
-
-    rb_hash_aset(modules, uri, obj);
-    xsltRegisterExtModule((unsigned char *)StringValuePtr(uri), initFunc, shutdownFunc);
-    return self;
-}
-
-VALUE cNokogiriXsltStylesheet ;
-void init_xslt_stylesheet()
-{
-  VALUE nokogiri;
-  VALUE klass;
-
-  nokogiri = rb_define_module("Nokogiri");
-  xslt = rb_define_module_under(nokogiri, "XSLT");
-  klass = rb_define_class_under(xslt, "Stylesheet", rb_cObject);
-
-  rb_iv_set(xslt, "@modules", rb_hash_new());
-
-  cNokogiriXsltStylesheet = klass;
-
-  rb_define_singleton_method(klass, "parse_stylesheet_doc", parse_stylesheet_doc, 1);
-  rb_define_singleton_method(xslt, "register", registr, 2);
-  rb_define_method(klass, "serialize", serialize, 1);
-  rb_define_method(klass, "transform", transform, -1);
-}

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

@@ -1,9 +0,0 @@
-#ifndef NOKOGIRI_XSLT_STYLESHEET
-#define NOKOGIRI_XSLT_STYLESHEET
-
-#include <nokogiri.h>
-
-void init_xslt_stylesheet();
-
-extern VALUE cNokogiriXsltStylesheet ;
-#endif

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

@@ -1,99 +0,0 @@
-module Nokogiri
-  module CSS
-    class Node
-      # Get the type of this node
-      attr_accessor :type
-      # Get the value of this node
-      attr_accessor :value
-
-      # Create a new Node with +type+ and +value+
-      def initialize type, value
-        @type = type
-        @value = value
-      end
-
-      # Accept +visitor+
-      def accept visitor
-        visitor.send(:"visit_#{type.to_s.downcase}", self)
-      end
-
-      ###
-      # Convert this CSS node to xpath with +prefix+ using +visitor+
-      def to_xpath prefix = '//', visitor = XPathVisitor.new
-        self.preprocess!
-        prefix + visitor.accept(self)
-      end
-
-      # Preprocess this node tree
-      def preprocess!
-        ### Deal with nth-child
-        matches = find_by_type(
-          [:CONDITIONAL_SELECTOR,
-            [:ELEMENT_NAME],
-            [:PSEUDO_CLASS,
-              [:FUNCTION]
-            ]
-          ]
-        )
-        matches.each do |match|
-          if match.value[1].value[0].value[0] =~ /^nth-(last-)?child/
-            tag_name = match.value[0].value.first
-            match.value[0].value = ['*']
-            match.value[1] = Node.new(:COMBINATOR, [
-              match.value[1].value[0],
-              Node.new(:FUNCTION, ['self(', tag_name])
-            ])
-          end
-        end
-
-        ### Deal with first-child, last-child
-        matches = find_by_type(
-          [:CONDITIONAL_SELECTOR,
-            [:ELEMENT_NAME], [:PSEUDO_CLASS]
-        ])
-        matches.each do |match|
-          if ['first-child', 'last-child'].include?(match.value[1].value.first)
-            which = match.value[1].value.first.gsub(/-\w*$/, '')
-            tag_name = match.value[0].value.first
-            match.value[0].value = ['*']
-            match.value[1] = Node.new(:COMBINATOR, [
-              Node.new(:FUNCTION, ["#{which}("]),
-              Node.new(:FUNCTION, ['self(', tag_name])
-            ])
-          elsif 'only-child' == match.value[1].value.first
-            tag_name = match.value[0].value.first
-            match.value[0].value = ['*']
-            match.value[1] = Node.new(:COMBINATOR, [
-              Node.new(:FUNCTION, ["#{match.value[1].value.first}("]),
-              Node.new(:FUNCTION, ['self(', tag_name])
-            ])
-          end
-        end
-
-        self
-      end
-
-      # Find a node by type using +types+
-      def find_by_type types
-        matches = []
-        matches << self if to_type == types
-        @value.each do |v|
-          matches += v.find_by_type(types) if v.respond_to?(:find_by_type)
-        end
-        matches
-      end
-
-      # Convert to_type
-      def to_type
-        [@type] + @value.map { |n|
-          n.to_type if n.respond_to?(:to_type)
-        }.compact
-      end
-
-      # Convert to array
-      def to_a
-        [@type] + @value.map { |n| n.respond_to?(:to_a) ? n.to_a : [n] }
-      end
-    end
-  end
-end