END_TEST
START_TEST (test_GroupsExtension_read_L3V1V1_defaultNS)
{
char *filename = safe_strcat(TestDataDirectory, "groups-example1-defaultNS.xml");
SBMLDocument *document = readSBMLFromFile(filename);
fail_unless(document->getPackageName() == "core");
Model *model = document->getModel();
document->printErrors();
fail_unless(model != NULL);
fail_unless(document->getNumErrors() == 0);
// get the Group
GroupsModelPlugin* mplugin = static_cast<GroupsModelPlugin*>(model->getPlugin("groups"));
fail_unless(mplugin != NULL);
fail_unless(mplugin->getNumGroups() == 1);
fail_unless(mplugin->getListOfGroups()->getPackageName() == "groups");
Group* group = mplugin->getGroup(0);
fail_unless(group->getId() == "ATP");
fail_unless(group->getSBOTermID() == "SBO:0000252");
fail_unless(group->getKind() == GROUP_KIND_CLASSIFICATION);
fail_unless(group->isSetKind() == true);
fail_unless(!strcmp(GroupKind_toString(group->getKind()), "classification"));
fail_unless(group->getNumMembers() == 2);
fail_unless(group->getPackageName() == "groups");
fail_unless(group->getListOfMembers()->getPackageName() == "groups");
Member* member = group->getMember(0);
fail_unless(member->getIdRef() == "ATPc");
fail_unless(member->getPackageName() == "groups");
member = group->getMember(1);
fail_unless(member->getIdRef() == "ATPm");
fail_unless(member->getPackageName() == "groups");
delete document;
safe_free(filename);
}
END_TEST
START_TEST (test_GroupsModelPlugin_copyNesting2)
{
//GroupsPkgNamespaces gpn;
//SBMLDocument doc(&gpn);
char *filename = safe_strcat(TestDataDirectory, "groups-nested1.xml");
SBMLDocument *document = readSBMLFromFile(filename);
Model* model = document->getModel();
fail_unless(model != NULL);
GroupsModelPlugin* mplugin = static_cast<GroupsModelPlugin*>(model->getPlugin("groups"));
fail_unless(mplugin != NULL);
fail_unless(mplugin->getNumGroups() == 4);
Group* group1 = mplugin->getGroup(0);
Group* group2 = mplugin->getGroup(1);
Group* group3 = mplugin->getGroup(2);
Group* group4 = mplugin->getGroup(3);
group3->getListOfMembers()->setSBOTerm(5);
mplugin->copyInformationToNestedLists();
fail_unless(!group1->getListOfMembers()->isSetSBOTerm());
fail_unless( group2->getListOfMembers()->getSBOTerm() == 5);
fail_unless( group3->getListOfMembers()->getSBOTerm() == 5);
fail_unless( group4->getListOfMembers()->getSBOTerm() == 252);
group4->getListOfMembers()->setNotes("These are some notes, v1.", true);
group3->getListOfMembers()->setNotes("These are some notes, v2.", true);
mplugin->copyInformationToNestedLists();
fail_unless(!group1->getListOfMembers()->isSetNotes());
fail_unless( group2->getListOfMembers()->getNotesString().find("These are some notes, v2.") != string::npos);
fail_unless( group3->getListOfMembers()->getNotesString().find("These are some notes, v2.") != string::npos);
fail_unless( group4->getListOfMembers()->getNotesString().find("These are some notes, v1.") != string::npos);
group4->getListOfMembers()->setAnnotation("This is a malformed annotation, v1.");
group3->getListOfMembers()->setAnnotation("This is a malformed annotation, v2.");
mplugin->copyInformationToNestedLists();
fail_unless(!group1->getListOfMembers()->isSetAnnotation());
fail_unless( group2->getListOfMembers()->getAnnotationString().find("This is a malformed annotation, v2.") != string::npos);
fail_unless( group3->getListOfMembers()->getAnnotationString().find("This is a malformed annotation, v2.") != string::npos);
fail_unless( group4->getListOfMembers()->getAnnotationString().find("This is a malformed annotation, v1.") != string::npos);
delete document;
safe_free((void*)(filename));
}
END_TEST
START_TEST (test_GroupsExtension_read_memberConstraints)
{
char *filename = safe_strcat(TestDataDirectory, "groups_speciestype_example.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 Group
GroupsModelPlugin* mplugin = static_cast<GroupsModelPlugin*>(model->getPlugin("groups"));
fail_unless(mplugin != NULL);
fail_unless(mplugin->getNumGroups() == 1);
fail_unless(mplugin->getListOfGroups()->getPackageName() == "groups");
Group* group = mplugin->getGroup(0);
fail_unless(group->getId() == "ATP");
fail_unless(group->getKind() == GROUP_KIND_CLASSIFICATION);
fail_unless(group->getNumMembers() == 2);
fail_unless(group->getNumMemberConstraints() == 3);
fail_unless(group->getPackageName() == "groups");
fail_unless(group->getListOfMembers()->getPackageName() == "groups");
fail_unless(group->getListOfMembers()->getSBOTermID() == "SBO:0000248");
Member* member = group->getMember(0);
fail_unless(member->getIdRef() == "ATPc");
fail_unless(member->getPackageName() == "groups");
member = group->getMember(1);
fail_unless(member->getIdRef() == "ATPm");
fail_unless(member->getPackageName() == "groups");
ListOfMemberConstraints* lomcs = group->getListOfMemberConstraints();
fail_unless(lomcs->getPackageName() == "groups");
fail_unless(lomcs->isSetMembersShareType() == true);
fail_unless(lomcs->getMembersShareType() == true);
MemberConstraint* mc = group->getMemberConstraint(0);
fail_unless(mc->isSetDistinctAttribute() == true);
fail_unless(mc->isSetIdenticalAttribute() == false);
fail_unless(mc->getDistinctAttribute() == "compartment");
fail_unless(mc->getPackageName() == "groups");
mc = group->getMemberConstraint(1);
fail_unless(mc->isSetDistinctAttribute() == false);
fail_unless(mc->isSetIdenticalAttribute() == true);
fail_unless(mc->getIdenticalAttribute() == "initialConcentration");
fail_unless(mc->getPackageName() == "groups");
mc = group->getMemberConstraint(2);
fail_unless(mc->isSetDistinctAttribute() == false);
fail_unless(mc->isSetIdenticalAttribute() == true);
fail_unless(mc->getIdenticalAttribute() == "constant");
fail_unless(mc->getPackageName() == "groups");
delete document;
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv){
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "groups") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
// SBMLNamespaces sbmlns(3,1,"groups",1,"GROUP");
//
SBMLNamespaces sbmlns(3,1,"groups",1);
//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
// adds a groups package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("groups",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(GroupsExtension::XmlnsL3V1V1,"groups");
//
// (2) Creates a GroupsPkgNamespaces object (SBMLNamespace derived class for
// groups package. The class is basically used for createing an SBase derived
// objects defined in the groups package) with the given SBML level, version,
// and package version
//
// GroupsPkgNamespaces sbmlns(3,1,1);
//
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
// create the Model
Model* model=document->createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("cytosol");
compartment->setConstant(true);
compartment=model->createCompartment();
compartment->setId("mitochon");
compartment->setConstant(true);
// create the Species
Species* species = model->createSpecies();
species->setId("ATPc");
species->setCompartment("cytosol");
species->setInitialConcentration(1);
species->setHasOnlySubstanceUnits(false);
species->setBoundaryCondition(false);
species->setConstant(false);
species = model->createSpecies();
species->setId("ATPm");
species->setCompartment("mitochon");
species->setInitialConcentration(2);
species->setHasOnlySubstanceUnits(false);
species->setBoundaryCondition(false);
species->setConstant(false);
// create the Groups
//
// Get a GroupsModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is SBasePlugin*, and
// thus the value needs to be casted for the corresponding derived class.
//
GroupsModelPlugin* mplugin = static_cast<GroupsModelPlugin*>(model->getPlugin("groups"));
//
// Creates a Group object via GroupsModelPlugin object.
//
Group* group = mplugin->createGroup();
group->setId("ATP");
group->setKind(GROUP_KIND_CLASSIFICATION);
group->setSBOTerm("SBO:0000252");
Member* member = group->createMember();
member->setIdRef("ATPc");
member = group->createMember();
member->setIdRef("ATPm");
writeSBML(document,"groups_example1.xml");
delete document;
}
