END_TEST
START_TEST(test_FbcExtension_convert_and_write)
{
string file(TestDataDirectory);
file += "/fbc_ga_example.xml";
SBMLDocument* document = readSBMLFromFile(file.c_str());
document->printErrors();
fail_unless(document->getNumErrors(LIBSBML_SEV_ERROR) == 0);
fail_unless(document->getModel() != NULL);
// convert to v2
{
ConversionProperties props;
props.addOption("convert fbc v1 to fbc v2", true);
props.addOption("strict", true);
int result = document->convert(props);
// ensure that all is well with the model
fail_unless(result == LIBSBML_OPERATION_SUCCESS);
fail_unless(document->getLevel() == 3);
fail_unless(document->getVersion() == 1);
fail_unless(document->getPlugin("fbc") != NULL);
fail_unless(document->getPlugin("fbc")->getPackageVersion() == 2);
}
// ensure that all the v1 stuff is no longer there
FbcModelPlugin* mplug = dynamic_cast<FbcModelPlugin*>(
document->getModel()->getPlugin("fbc"));
fail_unless(mplug != NULL);
fail_unless(mplug->isSetStrict());
fail_unless(mplug->getNumGeneAssociations() == 0);
fail_unless(mplug->getNumFluxBounds() == 0);
delete document;
}
Model* CompModelPlugin::flattenModel() const
{
//First make a copy of our parent (the model to be flattened):
const Model* parent = static_cast<const Model*>(getParentSBMLObject());
if (parent==NULL) {
return NULL;
}
//doc needs to be non-const so that the error messages can be updated. Otherwise, nothing changes.
SBMLDocument* doc = const_cast<SBMLDocument*>(getSBMLDocument());
if (doc==NULL) {
return NULL;
}
//Set the original document so that it can find the model definitions
//and external model definitions while we flatten.
Model* flat = parent->clone();
flat->setSBMLDocument(doc);
CompModelPlugin* flatplug =
static_cast<CompModelPlugin*>(flat->getPlugin(getPrefix()));
// Now instantiate its submodels and
// follow all renaming/deletion/replacement rules.
vector<const Model*> submods;
int success = flatplug->instantiateSubmodels();
if (success != LIBSBML_OPERATION_SUCCESS) {
//instantiateSubmodels sets its own error messages.
delete flat;
return NULL;
}
//Now start the aggregation process.
//This goes from the bottom up, calling 'appendFrom' iteratively
//(from the plugin).
for (unsigned int sm=0; sm<flatplug->getNumSubmodels(); sm++)
{
Model* submodel = flatplug->getSubmodel(sm)->getInstantiation();
if (submodel==NULL) {
//getInstantiation should be calling a cached value by now, but if not, it will set its own error messages.
delete flat;
return NULL;
}
CompModelPlugin* submodplug =
static_cast<CompModelPlugin*>(submodel->getPlugin(getPrefix()));
if (submodplug != NULL) {
//Strip the ports from the submodel, as we no longer need them.
while (submodplug->getNumPorts() > 0)
{
delete submodplug->removePort(0);
}
}
success = flat->appendFrom(submodel);
if (success != LIBSBML_OPERATION_SUCCESS) {
string error = "Unable to flatten model in CompModelPlugin::flattenModel: appending elements from the submodel '" + submodel->getId() + "' to the elements of the parent model failed.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error);
delete flat;
return NULL;
}
#ifdef LIBSBML_HAS_PACKAGE_FBC
// for an fbc v2 model we need to check that the model element
// in the flat document has the fbc:strict attribute
// note this can happen if the parent document did not have fbc but
// included a submodel from an external document that did
if (SBMLExtensionRegistry::isPackageEnabled("fbc"))
{
FbcModelPlugin *mplugin = static_cast<FbcModelPlugin*>
(flat->getPlugin("fbc"));
if (mplugin != NULL && mplugin->getPackageVersion() == 2
&& mplugin->isSetStrict() == false)
{
mplugin->setStrict(false);
}
}
#endif // LIBSBML_HAS_PACKAGE_FBC
}
// Now we clear the saved referenced elements in the local Port objects,
// but point them to the new object if necessary.
flatplug->resetPorts();
// Next, strip the package info from 'flat'.
// We're going to remove everything but the Ports:
flatplug->mListOfSubmodels.clear();
flatplug->clearReplacedElements();
flatplug->unsetReplacedBy();
List* allelements = flat->getAllElements();
vector<SBase*> nonReplacedElements;
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_REPLACEDBY ||
type==SBML_COMP_REPLACEDELEMENT ||
type==SBML_COMP_SBASEREF))
{
nonReplacedElements.push_back(element);
}
}
// delete the list
delete allelements;
for (unsigned int el=0; el<nonReplacedElements.size(); el++)
{
SBase* element = nonReplacedElements[el];
CompSBasePlugin* elplug =
static_cast<CompSBasePlugin*>(element->getPlugin(getPrefix()));
if (elplug != NULL)
{
elplug->clearReplacedElements();
elplug->unsetReplacedBy();
}
}
//Finally, unset the document again.
flat->setSBMLDocument(NULL);
return flat;
}