END_TEST
START_TEST (test_FbcExtension_read_L3V1V1_defaultNS)
{
char *filename = safe_strcat(TestDataDirectory, "fbc_example1_defaultNS.xml");
SBMLDocument *document = readSBMLFromFile(filename);
fail_unless(document->getPackageName() == "core");
Model *model = document->getModel();
fail_unless(model != NULL);
fail_unless(model->getPackageName() == "core");
fail_unless(document->getNumErrors() == 0);
// get the fbc plugin
FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));
fail_unless(mplugin != NULL);
fail_unless(mplugin->getNumObjectives() == 1);
fail_unless(mplugin->getListOfObjectives()->getPackageName() == "fbc");
Objective* objective = mplugin->getObjective(0);
fail_unless(objective->getId() == "obj1");
fail_unless(objective->getType() == "maximize");
fail_unless(objective->getNumFluxObjectives() == 1);
fail_unless(objective->getPackageName() == "fbc");
fail_unless(objective->getListOfFluxObjectives()->getPackageName() == "fbc");
FluxObjective* fluxObjective = objective->getFluxObjective(0);
fail_unless(fluxObjective->getReaction() == "J8");
fail_unless(fluxObjective->getPackageName() == "fbc");
fail_unless(fluxObjective->getCoefficient() == 1);
fail_unless(mplugin->getNumFluxBounds() == 1);
fail_unless(mplugin->getListOfFluxBounds()->getPackageName() == "fbc");
FluxBound* bound = mplugin->getFluxBound(0);
fail_unless(bound->getId() == "bound1");
fail_unless(bound->getPackageName() == "fbc");
fail_unless(bound->getReaction() == "J0");
fail_unless(bound->getOperation() == "equal");
fail_unless(bound->getValue() == 10);
delete document;
}
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;
}
int
FbcToCobraConverter::convert()
{
int result = LIBSBML_OPERATION_FAILED;
if (mDocument == NULL)
{
return LIBSBML_INVALID_OBJECT;
}
Model* mModel = mDocument->getModel();
if (mModel == NULL)
{
return LIBSBML_INVALID_OBJECT;
}
FbcModelPlugin *plugin =
static_cast<FbcModelPlugin*>(mDocument->getModel()->getPlugin("fbc"));
// if we have don't have a fbc model we cannot do the conversion
if (plugin == NULL || mDocument->getLevel() != 3)
{
return LIBSBML_OPERATION_FAILED;
}
// collect information
Model* model = mDocument->getModel();
map<const string, int> chargeMap;
map<const string, string> formulaMap;
for (unsigned int i = 0; i < model->getNumSpecies(); ++i)
{
Species* current = model->getSpecies(i);
const string& currentId = current->getId();
FbcSpeciesPlugin *splugin = static_cast<FbcSpeciesPlugin*>(current->getPlugin("fbc"));
if (splugin == NULL)
continue;
if (splugin->isSetCharge())
{
chargeMap[currentId] = splugin->getCharge();
}
if (splugin->isSetChemicalFormula())
{
formulaMap[currentId] = splugin->getChemicalFormula();
}
}
// create KineticLaw
for (unsigned int i = 0; i < model->getNumReactions(); ++i)
{
Reaction* reaction = model->getReaction(i);
if (reaction == NULL)
continue;
createKineticLawForReaction(reaction);
}
// update kinetic law from bounds
for (unsigned int i = 0; i < plugin->getNumFluxBounds(); ++i)
{
FluxBound *current = plugin->getFluxBound(i);
if (current == NULL)
continue;
Reaction* reaction = model->getReaction(current->getReaction());
if (reaction == NULL)
continue;
updateKineticLawFromBound(reaction, current);
}
setObjectiveCoefficient(plugin, model);
// disable package
mDocument->enablePackage("http://www.sbml.org/sbml/level3/version1/fbc/version1", "fbc",false);
// convert model to L2V1 (as L2V2 is the last model that had charge)
mDocument->setConversionValidators(AllChecksON & UnitsCheckOFF);
ConversionProperties prop(new SBMLNamespaces(2,1));
prop.addOption("strict", false, "should validity be preserved");
prop.addOption("ignorePackages", true, "convert even if packages are used");
prop.addOption("setLevelAndVersion", true, "convert the document to the given level and version");
int conversionResult = mDocument->convert(prop);
if (conversionResult != LIBSBML_OPERATION_SUCCESS)
return conversionResult;
// set charge on species
for (unsigned int i = 0; i < model->getNumSpecies(); ++i)
{
Species* current = model->getSpecies(i);
const string currentId = current->getId();
int charge = chargeMap[currentId];
if (charge != 0)
current->setCharge(charge);
const string formula = formulaMap[currentId];
if (!formula.empty())
{
current->setNotes( getNotesForFormula(formula) );
}
}
result = LIBSBML_OPERATION_SUCCESS;
return result;
}