Esempio n. 1
0
/**
 * Sets the type of an ASTNode based on the given MathML <cn> element.
 * Errors will be logged in the stream's SBMLErrorLog object.
 */
static void
setTypeCN (ASTNode& node, const XMLToken& element, XMLInputStream& stream)
{
  string type = "real";
  element.getAttributes().readInto("type", type);

  // here is the only place we might encounter the sbml:units attribute
  string units = "";
  element.getAttributes().readInto("units", units);

  if (type == "real")
  {
    double value = 0;
    istringstream isreal;
    isreal.str( stream.next().getCharacters() );
    isreal >> value;

    node.setValue(value);

    if (isreal.fail() 
      || node.isInfinity()
      || node.isNegInfinity()
      )
    {
      static_cast <SBMLErrorLog*>
        (stream.getErrorLog())->logError(FailedMathMLReadOfDouble,
          stream.getSBMLNamespaces()->getLevel(), 
          stream.getSBMLNamespaces()->getVersion());
    }

  }
Esempio n. 2
0
/**
 * Sets the type of an ASTNode based on the given MathML <ci> element.
 * Errors will be logged in the stream's SBMLErrorLog object.
 */
static void
setTypeCI (ASTNode& node, const XMLToken& element, XMLInputStream& stream)
{
  if (element.getName() == "csymbol")
  {
    string url;
    element.getAttributes().readInto("definitionURL", url);

    if ( url == URL_DELAY ) node.setType(AST_FUNCTION_DELAY);
    else if ( url == URL_TIME  ) node.setType(AST_NAME_TIME);
    else if ( url == URL_AVOGADRO  ) node.setType(AST_NAME_AVOGADRO);
    else 
    {
      static_cast <SBMLErrorLog*>
	        (stream.getErrorLog())->logError(BadCsymbolDefinitionURLValue,
          stream.getSBMLNamespaces()->getLevel(), 
          stream.getSBMLNamespaces()->getVersion());
    }
  }
  else if (element.getName() == "ci")
  {
    node.setDefinitionURL(element.getAttributes());
  }

  const string name = trim( stream.next().getCharacters() );
  node.setName( name.c_str() );
}
Esempio n. 3
0
void
ASTCnBase::addExpectedAttributes(ExpectedAttributes& attributes, 
                                     XMLInputStream& stream)
{
  ASTBase::addExpectedAttributes(attributes, stream);

  if (stream.getSBMLNamespaces() != NULL
    && stream.getSBMLNamespaces()->getLevel() > 2)
  {
    attributes.add("units");
  }

  attributes.add("type");
}
Esempio n. 4
0
bool
AnalyticVolume::readOtherXML (XMLInputStream& stream)
{
  bool          read = false;
  const string& name = stream.peek().getName();

  if (name == "math")
  {
    const XMLToken elem = stream.peek();
    const std::string prefix = checkMathMLNamespace(elem);

    if (stream.getSBMLNamespaces() == NULL)
    {
      stream.setSBMLNamespaces(new SBMLNamespaces(getLevel(), getVersion()));
    }

    delete mMath;
    mMath = readMathML(stream, prefix);
    read = true;
  }

  if (SBase::readOtherXML(stream))
  {
    read = true;
  }
  return read;
}
Esempio n. 5
0
bool 
ASTCnBase::read(XMLInputStream& stream, const std::string& )
{
  bool read = false;

  const XMLToken element = stream.next ();
  
  ExpectedAttributes expectedAttributes;
  addExpectedAttributes(expectedAttributes, stream);
  read = readAttributes(element.getAttributes(), expectedAttributes,
                        stream, element);

  string prefix;
  if (isSetUnits() == true)
  {
    prefix = element.getAttrPrefix(
      element.getAttrIndex("units", stream.getSBMLNamespaces()->getURI()));
	  
    setUnitsPrefix(prefix);
  }

  //return ASTBase::read(stream, reqd_prefix);

  return read;
}
Esempio n. 6
0
void
ASTBase::logError (XMLInputStream& stream, const XMLToken& element, SBMLErrorCode_t code,
          const std::string& msg)
{
  SBMLNamespaces* ns = stream.getSBMLNamespaces();
  if (ns != NULL)
  {
    static_cast <SBMLErrorLog*>
      (stream.getErrorLog())->logError(
      code,
      ns->getLevel(), 
      ns->getVersion(),
      msg, 
      element.getLine(), 
      element.getColumn());
  }
  else
  {
    static_cast <SBMLErrorLog*>
      (stream.getErrorLog())->logError(
      code, 
      SBML_DEFAULT_LEVEL, 
      SBML_DEFAULT_VERSION, 
      msg, 
      element.getLine(), 
      element.getColumn());
  }
}
void
ASTCiNumberNode::addExpectedAttributes(ExpectedAttributes& attributes, 
                                     XMLInputStream& stream)
{
  ASTBase::addExpectedAttributes(attributes, stream);

  SBMLNamespaces * sbmlns = stream.getSBMLNamespaces();
  if (sbmlns != NULL)
  {
    if (sbmlns->getLevel() > 2)
    {
      attributes.add("definitionURL");
    }
    else if (sbmlns->getLevel() == 2 && sbmlns->getVersion() == 5)
    {
      attributes.add("definitionURL");
    }
  }
}
Esempio n. 8
0
bool 
ASTBase::readAttributes(const XMLAttributes& attributes,
                       const ExpectedAttributes& expectedAttributes,
                               XMLInputStream& stream, const XMLToken& element)
{
  bool read = true;

  //
  // check that all attributes are expected
  //
  for (int i = 0; i < attributes.getLength(); i++)
  {
    std::string name   = attributes.getName(i);
    std::string uri    = attributes.getURI(i);
    std::string prefix = attributes.getPrefix(i);

    //
    // To allow prefixed attribute whose namespace doesn't belong to
    // core or extension package.
    //
    // (e.g. xsi:type attribute in Curve element in layout extension)
    //
    if (!prefix.empty())
    {
      if ( expectedAttributes.hasAttribute(prefix + ":" + name) ) continue;
    }

    if (!expectedAttributes.hasAttribute(name))
    {
      std::string message = "The attribute '" + name + "' is not permitted" +
        " on a <" + element.getName() + "> element.";
      if (name == "type")
      {
        logError(stream, element, DisallowedMathTypeAttributeUse, message);    
      }
      else if (name == "encoding")
      {
        logError(stream, element, DisallowedMathMLEncodingUse, message);    
      }
      else if (name == "definitionURL")
      {
        logError(stream, element, DisallowedDefinitionURLUse, message);    
      }
      else if (name == "units")
      {
        if (stream.getSBMLNamespaces() != NULL
          && stream.getSBMLNamespaces()->getLevel() > 2)
        {
          logError(stream, element, DisallowedMathUnitsUse, message);   
        }
        else
        {
          message = "The 'units' attribute was introduced in SBML Level 3.";
          logError(stream, element, InvalidMathMLAttribute, message);  
        }

      }
      else
      {
        logError(stream, element, InvalidMathElement, message);
      }

      // not sufficient to make the read bad
      //return false;
    }
  }


  
  string id; 
  string className;
  string style;

  attributes.readInto( "id"           , id        );
  attributes.readInto( "class"        , className );
  attributes.readInto( "style"        , style     );

  if (!id.empty())
  {
	  if (setId(id) != LIBSBML_OPERATION_SUCCESS)
    {
      read = false;
    }
  }

  if (!className.empty())
  {
	  if (setClass(className) != LIBSBML_OPERATION_SUCCESS)
    {
      read = false;
    }
  }

  if (!style.empty())
  {
	  if (setStyle(style) != LIBSBML_OPERATION_SUCCESS)
    {
      read = false;
    }
  }

  unsigned int i = 0;
  while (read == true && i < getNumPlugins())
  {
    read = getPlugin(i)->readAttributes(attributes, expectedAttributes, 
                                        stream, element, getExtendedType());
    i++;
  }


  return read;
}