void
PackageIdReplacementCheck::checkReferencedElement(ReplacedBy& repBy)
{
unsigned int numErrsB4 = repBy.getSBMLDocument()->getNumErrors();
SBase* refElem = repBy.getReferencedElement();
// if there is an issue with references the getReferencedElement
// will log errors and possibly fail
// we dont want to try any further
unsigned int numErrsAfter = repBy.getSBMLDocument()->getNumErrors();
if (numErrsB4 != numErrsAfter || refElem == NULL)
{
return;
}
SBase * parent = repBy.getParentSBMLObject();
if (parent->isSetId() == true && refElem->isSetId() == false)
{
logMissingIdAttribute(repBy, refElem, parent);
}
}
void
ClassReplacements::checkReferencedElement(ReplacedBy& repBy)
{
unsigned int numErrsB4 = repBy.getSBMLDocument()->getNumErrors();
SBase* refElem = repBy.getReferencedElement();
// if there is an issue with references the getReferencedElement
// will log errors and possibly fail
// we dont want to try any further
unsigned int numErrsAfter = repBy.getSBMLDocument()->getNumErrors();
if (numErrsB4 != numErrsAfter || refElem == NULL)
{
return;
}
SBase * parent = repBy.getParentSBMLObject();
if (refElem->getTypeCode() != parent->getTypeCode())
{
int refElemTC = refElem->getTypeCode();
// exception is anything with mathematical meaning
// may replace a parameter
if (parent->getTypeCode() == SBML_PARAMETER)
{
if (refElemTC == SBML_COMPARTMENT || refElemTC == SBML_SPECIES ||
refElemTC == SBML_SPECIES_REFERENCE || refElemTC == SBML_REACTION
|| refElemTC == SBML_LOCAL_PARAMETER)
{
return;
}
}
else if (parent->getTypeCode() == SBML_LOCAL_PARAMETER)
{
if (refElemTC == SBML_PARAMETER)
{
return;
}
}
logBadClassReplacement(repBy, refElem, parent);
}
}
int main(int argc,char** argv)
{
int retval = 0;
SBMLNamespaces sbmlns(3,1,"comp",1);
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
//Define the external model definition
CompSBMLDocumentPlugin* compdoc
= static_cast<CompSBMLDocumentPlugin*>(document->getPlugin("comp"));
compdoc->setRequired(true);
ExternalModelDefinition* extmod = compdoc->createExternalModelDefinition();
extmod->setId("ExtMod1");
extmod->setSource("enzyme_model.xml");
extmod->setModelRef("enzyme");
//Define the 'simple' model
ModelDefinition* mod1 = compdoc->createModelDefinition();
mod1->setId("simple");
Compartment* comp=mod1->createCompartment();
comp->setSpatialDimensions((unsigned int)3);
comp->setConstant(true);
comp->setId("comp");
comp->setSize(1L);
// We have to construct it this way because we get the comp
// plugin from it later.
Species spec(&sbmlns);
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
spec.setInitialConcentration(5);
mod1->addSpecies(&spec);
spec.setId("D");
spec.setInitialConcentration(10);
mod1->addSpecies(&spec);
Reaction rxn(&sbmlns);
rxn.setReversible(true);
rxn.setFast(false);
rxn.setId("J0");
SpeciesReference sr(&sbmlns);
sr.setConstant(true);
sr.setStoichiometry(1);
sr.setSpecies("S");
rxn.addReactant(&sr);
sr.setSpecies("D");
rxn.addProduct(&sr);
mod1->addReaction(&rxn);
CompModelPlugin* mod1plug
= static_cast<CompModelPlugin*>(mod1->getPlugin("comp"));
Port port;
port.setId("S_port");
port.setIdRef("S");
mod1plug->addPort(&port);
Port* port2 = mod1plug->createPort();
port2->setId("D_port");
port2->setIdRef("D");
port.setId("comp_port");
port.setIdRef("comp");
mod1plug->addPort(&port);
port.setId("J0_port");
port.setIdRef("J0");
mod1plug->addPort(&port);
// create the Model
Model* model=document->createModel();
model->setId("complexified");
// Set the submodels
CompModelPlugin* mplugin
= static_cast<CompModelPlugin*>(model->getPlugin("comp"));
Submodel* submod1 = mplugin->createSubmodel();
submod1->setId("A");
submod1->setModelRef("ExtMod1");
Submodel* submod2 = mplugin->createSubmodel();
submod2->setId("B");
submod2->setModelRef("simple");
Deletion* del = submod2->createDeletion();
del->setPortRef("J0_port");
// Synchronize the compartments
Compartment* mcomp=model->createCompartment();
mcomp->setSpatialDimensions((unsigned int)3);
mcomp->setConstant(true);
mcomp->setId("comp");
mcomp->setSize(1L);
CompSBasePlugin* compartplug
= static_cast<CompSBasePlugin*>(mcomp->getPlugin("comp"));
ReplacedElement re;
re.setIdRef("comp");
re.setSubmodelRef("A");
compartplug->addReplacedElement(&re);
re.setSubmodelRef("B");
re.unsetIdRef();
re.setPortRef("comp_port");
compartplug->addReplacedElement(&re);
//Synchronize the species
spec.setId("S");
spec.unsetInitialConcentration();
CompSBasePlugin* specplug
= static_cast<CompSBasePlugin*>(spec.getPlugin("comp"));
ReplacedElement* sre = specplug->createReplacedElement();
sre->setSubmodelRef("A");
sre->setIdRef("S");
ReplacedBy* srb = specplug->createReplacedBy();
srb->setSubmodelRef("B");
srb->setPortRef("S_port");
model->addSpecies(&spec);
spec.setId("D");
sre->setIdRef("D");
srb->setPortRef("D_port");
model->addSpecies(&spec);
writeSBMLToFile(document,"eg-ports.xml");
writeSBMLToFile(document,"spec_example3.xml");
delete document;
document = readSBMLFromFile("spec_example3.xml");
if (document == NULL)
{
cout << "Error reading back in file." << endl;
retval = -1;
}
else
{
document->setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, false);
document->checkConsistency();
if (document->getErrorLog()->getNumFailsWithSeverity(2) > 0
|| document->getErrorLog()->getNumFailsWithSeverity(3) > 0)
{
stringstream errorstream;
document->printErrors(errorstream);
cout << "Errors encoutered when round-tripping SBML file: \n"
<< errorstream.str() << endl;
retval = -1;
}
writeSBMLToFile(document, "spec_example3_rt.xml");
delete document;
}
#ifdef WIN32
if (retval != 0)
{
cout << "(Press any key to exit.)" << endl;
_getch();
}
#endif
return retval;
}
void
UnitReplacementCheck::checkReferencedElement(ReplacedBy& repBy)
{
unsigned int numErrsB4 = repBy.getSBMLDocument()->getNumErrors();
SBase* refElem = repBy.getReferencedElement();
// if there is an issue with references the getReferencedElement
// will log errors and possibly fail
// we dont want to try any further
unsigned int numErrsAfter = repBy.getSBMLDocument()->getNumErrors();
if (numErrsB4 != numErrsAfter || refElem == NULL)
{
return;
}
SBase * parent = repBy.getParentSBMLObject();
UnitDefinition *parentUnits = parent->getDerivedUnitDefinition();
//bool delparunit = parent->getTypeCode()==SBML_PARAMETER;
UnitDefinition *refElemUnits = refElem->getDerivedUnitDefinition();
//bool delrefunit = refElem->getTypeCode()==SBML_PARAMETER;
if (parentUnits == NULL || refElemUnits == NULL)
{
//if (delparunit)
//{
// delete parentUnits;
//}
//if (delrefunit)
//{
// delete refElemUnits;
//}
return;
}
if (parent->containsUndeclaredUnits() == true ||
refElem->containsUndeclaredUnits() == true)
{
//if (delparunit)
//{
// delete parentUnits;
//}
//if (delrefunit)
//{
// delete refElemUnits;
//}
return;
}
if (UnitDefinition::areIdentical(parentUnits, refElemUnits) == false)
{
logMismatchUnits(repBy, refElem, parent);
}
else
{
// if we have Compartments that have spatialDimensions but no units
// we can check this
if (parent->getTypeCode() == SBML_COMPARTMENT
&& parentUnits->getNumUnits() == 0
&& refElem->getTypeCode() == SBML_COMPARTMENT
&& refElemUnits->getNumUnits() == 0)
{
if (static_cast<Compartment *>(parent)->isSetSpatialDimensions() == true
&& static_cast<Compartment *>(refElem)->isSetSpatialDimensions() == true)
{
if (util_isEqual(
static_cast<Compartment *>(parent)->getSpatialDimensionsAsDouble(),
static_cast<Compartment *>(refElem)->getSpatialDimensionsAsDouble())
== 0)
{
logMismatchSpatialDimensions(repBy, refElem, parent);
}
}
}
}
//if (delparunit)
//{
// delete parentUnits;
//}
//if (delrefunit)
//{
// delete refElemUnits;
//}
}
void
CompIdBase::checkId (const ReplacedBy& x)
{
if (x.isSetId()) doCheckId(x.getId(), x);
}
