/*
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given @p id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
CiElementMathCheck::getMessage (const ASTNode& node, const SBase& object)
{
ostringstream msg;
//msg << getPreamble();
char * formula = SBML_formulaToString(&node);
msg << "The formula '" << formula;
msg << "' in the " << getFieldname() << " element of the <" << object.getElementName();
msg << "> ";
switch(object.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (object.isSetId()) {
msg << "with id '" << object.getId() << "' ";
}
break;
}
if (object.getLevel() == 2 && object.getVersion() == 1)
msg << "uses '" << node.getName() << "' that is not the id of a species/compartment/parameter.";
else if (object.getLevel() < 3)
msg << "uses '" << node.getName() << "' that is not the id of a species/compartment/parameter/reaction.";
else
msg << "uses '" << node.getName() << "' that is not the id of a species/compartment/parameter/reaction/speciesReference.";
safe_free(formula);
return msg.str();
}
/*
* Logs a constraint failure to the validator for the given SBML object.
* The parameter message is used instead of the constraint's member
* variable msg.
*/
void
VConstraint::logFailure (const SBase& object, const std::string& message)
{
std::string pkg = object.getPackageName();
unsigned int pkgVersion = object.getPackageVersion();
if (mId > 99999 && pkg == "core")
{
// we are dealing with a core object that is logging errors
// relating to a package
// need to work out which pkg
unsigned int offset = (unsigned int)(floor((double)mId/100000.0)) * 100000;
if (offset == 9900000)
{
// we are dealing with the strict units validator
mId = mId - offset;
}
else
{
// it is possible that the object does not have a direct plugin
// it may the child of an object that does
// so lets cut straight to the parent document
const SBMLDocument * doc = object.getSBMLDocument();
if (doc != NULL)
{
for (unsigned int i = 0; i < doc->getNumPlugins(); i++)
{
const SBMLExtension * ext = doc->getPlugin(i)->getSBMLExtension();
if (ext->getErrorIdOffset() == offset)
{
pkg = doc->getPlugin(i)->getPackageName();
pkgVersion = doc->getPlugin(i)->getPackageVersion();
break;
}
}
}
}
}
SBMLError error = SBMLError( mId, object.getLevel(), object.getVersion(),
message, object.getLine(), object.getColumn(),
LIBSBML_SEV_ERROR, LIBSBML_CAT_SBML, pkg, pkgVersion);
if (error.getSeverity() != LIBSBML_SEV_NOT_APPLICABLE)
mValidator.logFailure(error);
/* ( SBMLError( mId, object.getLevel(), object.getVersion(),
message, object.getLine(), object.getColumn(),
LIBSBML_SEV_ERROR, LIBSBML_CAT_SBML ));*/
}
/*
* Logs a constraint failure to the validator for the given SBML object.
* The parameter message is used instead of the constraint's member
* variable msg.
*/
void
VConstraint::logFailure (const SBase& object, const std::string& message)
{
if (&object == NULL || &message == NULL) return;
SBMLError error = SBMLError( mId, object.getLevel(), object.getVersion(),
message, object.getLine(), object.getColumn() );
if (error.getSeverity() != LIBSBML_SEV_NOT_APPLICABLE)
mValidator.logFailure(error);
/* ( SBMLError( mId, object.getLevel(), object.getVersion(),
message, object.getLine(), object.getColumn(),
LIBSBML_SEV_ERROR, LIBSBML_CAT_SBML ));*/
}
/**
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
CiElementMathCheck::getMessage (const ASTNode& node, const SBase& object)
{
ostringstream msg;
//msg << getPreamble();
char * formula = SBML_formulaToString(&node);
msg << "\nThe formula '" << formula;
msg << "' in the " << getFieldname() << " element of the " << getTypename(object);
if (object.getLevel() == 2 && object.getVersion() == 1)
msg << " uses '" << node.getName() << "' that is not the id of a species/compartment/parameter.";
else
msg << " uses '" << node.getName() << "' that is not the id of a species/compartment/parameter/reaction.";
safe_free(formula);
return msg.str();
}