void checkFbc(FbcModelPlugin* fbcmodplug, set<string>& components, set<string>& tests, const map<string, vector<double> >& results)
{
if (fbcmodplug->isSetStrict() && fbcmodplug->getStrict() == false) {
tests.insert("fbc:NonStrict");
}
List* allElements = fbcmodplug->getAllElements();
for (unsigned int e=0; e<allElements->getSize(); e++) {
SBase* element = static_cast<SBase*>(allElements->get(e));
FluxBound* fluxBound;
Objective* objective;
switch(element->getTypeCode()) {
case SBML_FBC_FLUXBOUND:
components.insert("fbc:FluxBound");
fluxBound = static_cast<FluxBound*>(element);
if (fluxBound->isSetOperation()) {
if (fluxBound->getOperation() == "lessEqual") {
tests.insert("fbc:BoundLessEqual");
}
else if (fluxBound->getOperation() == "greaterEqual") {
tests.insert("fbc:BoundGreaterEqual");
}
else if (fluxBound->getOperation() == "equal") {
tests.insert("fbc:BoundEqual");
}
}
break;
case SBML_FBC_OBJECTIVE:
components.insert("fbc:Objective");
objective = static_cast<Objective*>(element);
if (objective->isSetType()) {
if (objective->getType() == "maximize") {
tests.insert("fbc:MaximizeObjective");
}
else {
tests.insert("fbc:MinimizeObjective");
}
}
break;
case SBML_FBC_FLUXOBJECTIVE:
components.insert("fbc:FluxObjective");
break;
default:
break;
}
}
}
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;
}
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;
}
END_TEST
START_TEST(test_FbcExtension_create_and_write_new_geneassociation
)
{
FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 2);
// create the document
SBMLDocument document(sbmlns);
document.setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.setConsistencyChecks(LIBSBML_CAT_MODELING_PRACTICE, false);
// create the Model
Model* model = document.createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("compartment");
compartment->setConstant(true);
compartment->setSize(1);
// create the Species
Species* species = model->createSpecies();
species->setId("Node1");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species = model->createSpecies();
species->setId("Node2");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
Reaction* reaction = model->createReaction();
reaction->setId("J0");
reaction->setReversible(false);
SpeciesReference* reactant = reaction->createReactant();
reactant->setSpecies("Node0");
reactant->setStoichiometry(1);
SpeciesReference* product = reaction->createProduct();
product->setSpecies("Node1");
product->setStoichiometry(1);
// use fbc
FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));
fail_unless(mplugin != NULL);
FluxBound* bound = mplugin->createFluxBound();
bound->setId("bound1");
bound->setReaction("J0");
bound->setOperation("equal");
bound->setValue(10);
Objective* objective = mplugin->createObjective();
objective->setId("obj1");
objective->setType("maximize");
FluxObjective* fluxObjective = objective->createFluxObjective();
fluxObjective->setReaction("J0");
fluxObjective->setCoefficient(1);
FbcReactionPlugin* rplug = dynamic_cast<FbcReactionPlugin*>(reaction->getPlugin("fbc"));
fail_unless(rplug != NULL);
GeneProductAssociation * ga = rplug->createGeneProductAssociation();
ga->setId("ga1");
ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079");
fail_unless(ga->getAssociation() != NULL);
fail_unless(mplugin->getNumGeneProducts() == 5);
ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079");
fail_unless(ga->getAssociation() != NULL);
fail_unless(mplugin->getNumGeneProducts() == 5);
delete sbmlns;
}
END_TEST
START_TEST(test_FbcExtension_create_and_write_L3V1V1)
{
FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 1);
// create the document
SBMLDocument *document = new SBMLDocument(sbmlns);
delete sbmlns;
// create the Model
Model* model = document->createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("compartment");
compartment->setConstant(true);
compartment->setSize(1);
// create the Species
Species* species = model->createSpecies();
species->setId("Node1");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species = model->createSpecies();
species->setId("Node2");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
Reaction* reaction = model->createReaction();
reaction->setId("J0");
reaction->setReversible(false);
SpeciesReference* reactant = reaction->createReactant();
reactant->setSpecies("Node0");
reactant->setStoichiometry(1);
SpeciesReference* product = reaction->createProduct();
product->setSpecies("Node1");
product->setStoichiometry(1);
// use fbc
FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));
fail_unless(mplugin != NULL);
FluxBound* bound = mplugin->createFluxBound();
bound->setId("bound1");
bound->setReaction("J0");
bound->setOperation("equal");
bound->setValue(10);
Objective* objective = mplugin->createObjective();
objective->setId("obj1");
objective->setType("maximize");
FluxObjective* fluxObjective = objective->createFluxObjective();
fluxObjective->setReaction("J0");
fluxObjective->setCoefficient(1);
string s1 = writeSBMLToStdString(document);
// check clone()
SBMLDocument* document2 = document->clone();
string s2 = writeSBMLToStdString(document2);
fail_unless(s1 == s2);
// check operator=
Model m = *(document->getModel());
document2->setModel(&m);
s2 = writeSBMLToStdString(document2);
fail_unless(s1 == s2);
delete document2;
delete document;
}
