C++ SBMLError类代码示例

/*
 * 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 ));*/

}

int CompModelPlugin::saveAllReferencedElements(set<SBase*> uniqueRefs, set<SBase*> replacedBys)
{
  SBMLDocument* doc = getSBMLDocument();
  Model* model = static_cast<Model*>(getParentSBMLObject());
  if (model==NULL) {
    if (doc) {
      string error = "Unable to discover any referenced elements in CompModelPlugin::saveAllReferencedElements: no Model parent of the 'comp' model plugin.";
      doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error);
    }
    return LIBSBML_OPERATION_FAILED;
  }
  int ret = LIBSBML_OPERATION_SUCCESS;

  //Get a list of everything, pull out anything that's a deletion, replacement, or port, and save what they're pointing to.
  //At the same time, make sure that no two things point to the same thing.
  set<SBase*> RE_deletions = set<SBase*>(); //Deletions only point to things in the same model.
  List* allElements = model->getAllElements();
  string modname = "the main model in the document";
  if (model->isSetId()) {
    modname = "the model '" + model->getId() + "'";
  }
  set<SBase*> todelete;
  for (unsigned int el=0; el<allElements->getSize(); el++) {
    SBase* element = static_cast<SBase*>(allElements->get(el));
    int type = element->getTypeCode();
    if (type==SBML_COMP_DELETION ||
        type==SBML_COMP_REPLACEDBY ||
        type==SBML_COMP_REPLACEDELEMENT ||
        type==SBML_COMP_PORT) {
          //Don't worry about SBML_COMP_SBASEREF because they're all children of one of the above types.
          SBaseRef* reference = static_cast<SBaseRef*>(element);
          ReplacedElement* re = static_cast<ReplacedElement*>(element);
          ret = reference->saveReferencedElement();
          if (ret != LIBSBML_OPERATION_SUCCESS) 
          {
            if (type != SBML_COMP_REPLACEDBY && doc) 
            {
              SBMLErrorLog* errlog = doc->getErrorLog();
              SBMLError* lasterr = const_cast<SBMLError*>
                (doc->getErrorLog()->getError(doc->getNumErrors()-1));
              if ( (errlog->contains(UnrequiredPackagePresent) || 
                    errlog->contains(RequiredPackagePresent))) 
              {
                if ( lasterr->getErrorId() == CompIdRefMustReferenceObject)
                {
                   //Change the error into a warning
                   string fullmsg = lasterr->getMessage() 
                     + "  However, this may be because of the unrecognized "
                     + "package present in this document:  ignoring this "
                     + "element and flattening anyway.";
                   errlog->remove(lasterr->getErrorId());
                   errlog->logPackageError("comp", 
                     CompIdRefMayReferenceUnknownPackage, getPackageVersion(), 
                     getLevel(), getVersion(), fullmsg, element->getLine(), 
                     element->getColumn(), LIBSBML_SEV_WARNING);
                }
                else if ( lasterr->getErrorId() == CompMetaIdRefMustReferenceObject)
                {
                   //Change the error into a warning
                   string fullmsg = lasterr->getMessage() 
                     + "  However, this may be because of the unrecognized "
                     + "package present in this document:  ignoring this "
                     + "element and flattening anyway.";
                   errlog->remove(lasterr->getErrorId());
                   errlog->logPackageError("comp", 
                     CompMetaIdRefMayReferenceUnknownPkg, getPackageVersion(), 
                     getLevel(), getVersion(), fullmsg, element->getLine(), 
                     element->getColumn(), LIBSBML_SEV_WARNING);
                }
              }
              //Whether or not we could figure out the error, we can always still continue flattening.
              todelete.insert(element);
              continue;
            }
            else {
              delete allElements;
              return ret;
            }
          }
          SBase* direct = reference->getDirectReference();
          bool adddirect = true;
          if (type == SBML_COMP_REPLACEDBY) {
            SBase* rbParent = reference->getParentSBMLObject();
            if (uniqueRefs.insert(rbParent).second == false) {
              if (doc) {
                string error = "Error discovered in CompModelPlugin::saveAllReferencedElements when checking " + modname + ": a <" + rbParent->getElementName() + "> ";
                if (direct->isSetId()) {
                  error += "with the id '" + rbParent->getId() + "'";
                  if (rbParent->isSetMetaId()) {
                    error += ", and the metaid '" + rbParent->getMetaId() + "'";
                  }
                }
                else if (rbParent->isSetMetaId()) {
                  error += "with the metaId '" + rbParent->getMetaId() + "'";
                }
                error += " has a <replacedBy> child and is also pointed to by a <port>, <deletion>, <replacedElement>, or one or more <replacedBy> objects.";
                doc->getErrorLog()->logPackageError("comp", CompNoMultipleReferences, getPackageVersion(), getLevel(), getVersion(), error);
              }
              delete allElements;
              return LIBSBML_OPERATION_FAILED;
//.........这里部分代码省略.........

 bool operator() (const SBMLError& msg) {
     return msg.getErrorId() == id;
 }

/*
 * Adds the given SBMLError to the log.
 *
 * @param error SBMLError, the error to be logged.
 */
void
SBMLErrorLog::add (const SBMLError& error)
{
  if (error.getSeverity() != LIBSBML_SEV_NOT_APPLICABLE)
    XMLErrorLog::add(error);
}

LIBSBML_CPP_NAMESPACE_USE

/** @endcond */


CK_CPPSTART



START_TEST (test_SBMLError_create)
{
  SBMLError* error = new SBMLError;
  fail_unless( error != NULL );
  delete error;

  error = new SBMLError(EmptyListInReaction);
  fail_unless( error->getErrorId()  == EmptyListInReaction );
  fail_unless( error->getSeverity() == LIBSBML_SEV_ERROR );
  fail_unless( error->getSeverityAsString() == "Error" );
  fail_unless( error->getCategory() == LIBSBML_CAT_SBML );
  fail_unless( error->getCategoryAsString() == "General SBML conformance");
  fail_unless( error->isValid() == true);
  delete error;

  error = new SBMLError(OverdeterminedSystem, 2, 1);
  fail_unless( error->getErrorId()  == OverdeterminedSystem );
  fail_unless( error->getSeverity() == LIBSBML_SEV_WARNING );
  fail_unless( error->getSeverityAsString() == "Warning" );
  fail_unless( error->getCategory() == LIBSBML_CAT_OVERDETERMINED_MODEL );
  fail_unless( error->getCategoryAsString() == "Overdetermined model");
  fail_unless( error->isValid() == true);
  delete error;

  error = new SBMLError(OffsetNoLongerValid, 2, 2);
  fail_unless( error->getErrorId()  == OffsetNoLongerValid );
  fail_unless( error->getSeverity() == LIBSBML_SEV_ERROR );
  fail_unless( error->getSeverityAsString() == "Error" );
  fail_unless( error->getCategory() == LIBSBML_CAT_GENERAL_CONSISTENCY );
  fail_unless( error->getCategoryAsString() == "SBML component consistency");
  fail_unless( error->isValid() == true);
  delete error;

  error = new SBMLError(NoSBOTermsInL1, 2, 2);
  fail_unless( error->getErrorId()  == NoSBOTermsInL1 );
  fail_unless( error->getSeverity() == LIBSBML_SEV_WARNING );
  fail_unless( error->getSeverityAsString() == "Warning" );
  fail_unless( error->getCategory() == LIBSBML_CAT_SBML_L1_COMPAT );
  fail_unless( error->getCategoryAsString() == "Translation to SBML L1V2");
  fail_unless( error->isValid() == true);
  delete error;

  error = new SBMLError(DisallowedMathMLEncodingUse, 2, 2);
  fail_unless( error->getErrorId()  == DisallowedMathMLEncodingUse );
  fail_unless( error->getSeverity() == LIBSBML_SEV_ERROR );
  fail_unless( error->getSeverityAsString() == "Error" );
  fail_unless( error->getCategory() == LIBSBML_CAT_MATHML_CONSISTENCY );
  fail_unless( error->getShortMessage() == "Use of the MathML 'encoding' attribute is not allowed on this element");
  fail_unless( error->isValid() == true);
  delete error;

  error = new SBMLError(DisallowedMathMLEncodingUse, 1, 2);
  fail_unless( error->getErrorId()  == DisallowedMathMLEncodingUse );
  fail_unless( error->getSeverity() == LIBSBML_SEV_NOT_APPLICABLE );
  fail_unless( error->getCategory() == LIBSBML_CAT_MATHML_CONSISTENCY );
  fail_unless( error->isValid() == true);
  delete error;

  error = new SBMLError(UnknownError, 2, 4);
  fail_unless( error->getErrorId()  == UnknownError );
  fail_unless( error->getSeverity() == LIBSBML_SEV_FATAL );
  fail_unless( error->getSeverityAsString() == "Fatal" );
  fail_unless( error->getCategory() == LIBSBML_CAT_INTERNAL );
  fail_unless( error->getShortMessage() == "Encountered unknown internal libSBML error");
  fail_unless( error->isValid() == true);
  delete error;

  error = new SBMLError(70912, 2, 4);
  fail_unless( error->getErrorId()  == 70912 );
  fail_unless( error->getSeverity() == LIBSBML_SEV_WARNING );
  fail_unless( error->getSeverityAsString() == "Warning" );
  fail_unless( error->getCategory() == LIBSBML_CAT_INTERNAL );
  fail_unless( error->getShortMessage() == "Encountered unknown internal libSBML error");
  fail_unless( error->isValid() == false);
  delete error;
}