public void test_SBMLConvertStrict_convertNonStrictUnits()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
c.setConstant(false);
Parameter p = m.createParameter();
p.setId("p");
p.setUnits("mole");
ASTNode math = libsbml.parseFormula("p");
Rule ar = m.createAssignmentRule();
ar.setVariable("c");
ar.setMath(math);
assertTrue(d.setLevelAndVersion(2, 1, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 2, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 3, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(1, 2, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
d = null;
}
public void test_SBMLConvertStrict_convertNonStrictSBO()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
c.setConstant(false);
(c).setSBOTerm(64);
assertTrue(d.setLevelAndVersion(2, 3, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 2, true) == false);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
assertTrue(d.setLevelAndVersion(2, 1, true) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
Compartment c1 = d.getModel().getCompartment(0);
assertTrue((c1).getSBOTerm() == -1);
assertTrue(d.setLevelAndVersion(1, 2, true) == true);
assertTrue(d.getLevel() == 1);
assertTrue(d.getVersion() == 2);
Compartment c2 = d.getModel().getCompartment(0);
assertTrue((c2).getSBOTerm() == -1);
d = null;
}
public void test_SBMLDocument_setLevelAndVersion()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m1 = new Model(2, 2);
d.setModel(m1);
assertTrue(d.setLevelAndVersion(2, 3, false) == true);
assertTrue(d.setLevelAndVersion(2, 1, false) == true);
assertTrue(d.setLevelAndVersion(1, 2, false) == true);
assertTrue(d.setLevelAndVersion(1, 1, false) == false);
d = null;
}
public void test_SBMLConvert_invalidLevelVersion()
{
SBMLDocument d = new SBMLDocument(2, 1);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
c.setId(sid);
c.setSize(1.2);
c.setUnits("volume");
assertTrue(d.setLevelAndVersion(1, 3, true) == false);
assertTrue(d.setLevelAndVersion(2, 7, true) == false);
assertTrue(d.setLevelAndVersion(3, 5, true) == false);
assertTrue(d.setLevelAndVersion(4, 1, true) == false);
}
public void test_SBMLConvert_convertToL2_SBMLDocument()
{
SBMLDocument d = new SBMLDocument(1, 2);
assertTrue(d.setLevelAndVersion(2, 1, false) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
assertTrue(d.setLevelAndVersion(2, 2, false) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 2);
assertTrue(d.setLevelAndVersion(2, 3, false) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 3);
d = null;
}
public void test_SBMLConvertStrict_convertToL1()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
(m).setMetaId("_m");
Compartment c = m.createCompartment();
c.setId("c");
(c).setSBOTerm(240);
Species s = m.createSpecies();
s.setId("s");
s.setCompartment("c");
assertTrue(d.setLevelAndVersion(1, 2, true) == true);
assertTrue(d.getLevel() == 1);
assertTrue(d.getVersion() == 2);
Model m1 = d.getModel();
assertTrue((m1).getMetaId() == "");
Compartment c1 = m1.getCompartment(0);
assertTrue((c1).getSBOTerm() == -1);
Species s1 = m1.getSpecies(0);
assertTrue(s1.getHasOnlySubstanceUnits() == false);
d = null;
}
public void test_SBMLConvert_convertToL3_stoichiometryMath()
{
SBMLDocument d = new SBMLDocument(2, 1);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Species s = m.createSpecies();
s.setId("s");
s.setCompartment("c");
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
sr.setSpecies("s");
StoichiometryMath sm = sr.createStoichiometryMath();
ASTNode ast = libsbml.parseFormula("c*2");
sm.setMath(ast);
assertTrue(m.getNumRules() == 0);
assertTrue(sr.isSetId() == false);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
m = d.getModel();
r = m.getReaction(0);
sr = r.getReactant(0);
assertTrue(m.getNumRules() == 1);
assertTrue(sr.isSetId() == true);
Rule rule = m.getRule(0);
assertTrue((rule.getVariable() == sr.getId()));
d = null;
}
public void test_SBMLConvert_convertToL3_localParameters()
{
SBMLDocument d = new SBMLDocument(1, 2);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Species s = m.createSpecies();
s.setId("s");
s.setCompartment("c");
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
sr.setSpecies("s");
KineticLaw kl = r.createKineticLaw();
kl.setFormula("s*k");
Parameter p = kl.createParameter();
p.setId("k");
assertTrue(kl.getNumLocalParameters() == 0);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
m = d.getModel();
r = m.getReaction(0);
kl = r.getKineticLaw();
assertTrue(kl.getNumLocalParameters() == 1);
LocalParameter lp = kl.getLocalParameter(0);
d = null;
}
public void test_SBMLDocument_clone()
{
SBMLDocument o1 = new SBMLDocument();
o1.setLevelAndVersion(1, 1, false);
Model m = new Model(1, 1);
m.createCompartment();
m.createSpecies();
m.createReaction();
m.setId("foo");
o1.setModel(m);
assertTrue(o1.getLevel() == 1);
assertTrue(o1.getVersion() == 1);
assertTrue(o1.getModel().getId() == "foo");
assertTrue(o1.getModel().getLevel() == 1);
assertTrue(o1.getModel().getVersion() == 1);
assertTrue(o1.getModel().getSBMLDocument() == o1);
SBMLDocument o2 = o1.clone();
assertTrue(o2.getLevel() == 1);
assertTrue(o2.getVersion() == 1);
assertTrue(o2.getModel().getId() == "foo");
assertTrue(o2.getModel().getLevel() == 1);
assertTrue(o2.getModel().getVersion() == 1);
assertTrue(o2.getModel().getSBMLDocument() == o2);
o2 = null;
o1 = null;
}
public void test_SBMLConvertStrict_convertL1ParamRule()
{
SBMLDocument d = new SBMLDocument(1, 2);
Model m = d.createModel();
Compartment c = m.createCompartment();
c.setId("c");
Parameter p = m.createParameter();
p.setId("p");
Parameter p1 = m.createParameter();
p1.setId("p1");
ASTNode math = libsbml.parseFormula("p");
Rule ar = m.createAssignmentRule();
ar.setVariable("p1");
ar.setMath(math);
ar.setUnits("mole");
assertTrue(d.setLevelAndVersion(2, 1, true) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
Rule r1 = d.getModel().getRule(0);
assertTrue(r1.getUnits() == "");
d = null;
}
public void test_SBMLConvert_convertToL1_Species_Concentration()
{
SBMLDocument d = new SBMLDocument(2, 1);
Model m = d.createModel();
string sid = "C";
Compartment c = new Compartment(2, 1);
Species s = new Species(2, 1);
c.setId(sid);
c.setSize(1.2);
m.addCompartment(c);
s.setId("s");
s.setCompartment(sid);
s.setInitialConcentration(2.34);
m.addSpecies(s);
assertTrue(d.setLevelAndVersion(1, 2, true) == true);
Species s1 = m.getSpecies(0);
assertTrue(s1 != null);
assertTrue(("C" == s1.getCompartment()));
assertTrue(m.getCompartment("C").getSize() == 1.2);
assertTrue(s1.getInitialConcentration() == 2.34);
assertTrue(s1.isSetInitialConcentration() == true);
d = null;
}
public void test_SBMLConvert_convertToL3_event()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
Event e = m.createEvent();
Event e1;
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
e1 = m.getEvent(0);
assertTrue(e1.hasRequiredAttributes() == true);
d = null;
}
public void test_SBMLDocument_setLevelAndVersion_Error()
{
SBMLDocument d = new SBMLDocument();
d.setLevelAndVersion(2, 1, true);
Model m1 = new Model(2, 1);
Unit u = new Unit(2, 1);
u.setKind(libsbml.UnitKind_forName("mole"));
u.setOffset(3.2);
UnitDefinition ud = new UnitDefinition(2, 1);
ud.setId("ud");
ud.addUnit(u);
m1.addUnitDefinition(ud);
d.setModel(m1);
assertTrue(d.setLevelAndVersion(2, 2, true) == false);
assertTrue(d.setLevelAndVersion(2, 3, true) == false);
assertTrue(d.setLevelAndVersion(1, 2, true) == false);
assertTrue(d.setLevelAndVersion(1, 1, true) == false);
d = null;
}
public void test_SBMLConvert_convertToL3_parameter()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
string sid = "C";
Parameter p = m.createParameter();
Parameter p1;
p.setId(sid);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
p1 = m.getParameter(0);
assertTrue(p1.hasRequiredAttributes() == true);
d = null;
}
public void test_SBMLConvert_convertToL3_reaction()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
string sid = "C";
Reaction r = m.createReaction();
r.setId(sid);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
Reaction r1 = m.getReaction(0);
assertTrue(r1.hasRequiredAttributes() == true);
d = null;
}
public void test_SBMLConvert_convertToL3_reactant()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
Reaction r = m.createReaction();
SpeciesReference sr = r.createReactant();
SpeciesReference sr1;
sr.setSpecies("s");
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
sr1 = m.getReaction(0).getReactant(0);
assertTrue(sr1.hasRequiredAttributes() == true);
d = null;
}
public void test_SBMLConvert_convertToL3_compartment()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
string sid = "C";
Compartment c = m.createCompartment();
Compartment c1;
c.setId(sid);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
c1 = m.getCompartment(0);
assertTrue(c1.hasRequiredAttributes() == true);
d = null;
}
public void test_SBMLDocument_copyConstructor()
{
SBMLDocument o1 = new SBMLDocument();
o1.setLevelAndVersion(2, 1, false);
assertTrue(o1.getLevel() == 2);
assertTrue(o1.getVersion() == 1);
SBMLDocument o2 = new SBMLDocument(o1);
assertTrue(o2.getLevel() == 2);
assertTrue(o2.getVersion() == 1);
o2 = null;
o1 = null;
}
public void test_SBMLDocument_setLevelAndVersion_UnitsError()
{
SBMLDocument d = new SBMLDocument();
d.setLevelAndVersion(2, 4, false);
Model m1 = d.createModel();
Compartment c = m1.createCompartment();
c.setId("c");
Parameter p = m1.createParameter();
p.setId("p");
p.setUnits("mole");
Rule r = m1.createAssignmentRule();
r.setVariable("c");
r.setFormula("p*p");
assertTrue(d.setLevelAndVersion(2, 2, false) == true);
assertTrue(d.setLevelAndVersion(2, 3, false) == true);
assertTrue(d.setLevelAndVersion(1, 2, false) == true);
assertTrue(d.setLevelAndVersion(1, 1, false) == false);
d = null;
}
public void test_SBMLConvert_convertToL3_species()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
string sid = "C";
Species s = m.createSpecies();
Species s1;
s.setId(sid);
s.setCompartment("comp");
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
s1 = m.getSpecies(0);
assertTrue(s1.hasRequiredAttributes() == true);
d = null;
}
public void test_SBMLDocument_assignmentOperator()
{
SBMLDocument o1 = new SBMLDocument();
o1.setLevelAndVersion(2, 1, false);
assertTrue(o1.getLevel() == 2);
assertTrue(o1.getVersion() == 1);
SBMLDocument o2 = new SBMLDocument();
o2 = o1;
assertTrue(o2.getLevel() == 2);
assertTrue(o2.getVersion() == 1);
o2 = null;
o1 = null;
}
public void test_SBMLConvert_convertFromL3_modelUnits()
{
UnitDefinition ud;
SBMLDocument d = new SBMLDocument(3, 1);
Model m = d.createModel();
m.setVolumeUnits("litre");
assertTrue(m.getNumUnitDefinitions() == 0);
assertTrue(d.setLevelAndVersion(2, 4, false) == true);
m = d.getModel();
assertTrue(m.getNumUnitDefinitions() == 1);
ud = m.getUnitDefinition(0);
assertTrue(("volume" == ud.getId()));
assertTrue(ud.getNumUnits() == 1);
assertTrue(ud.getUnit(0).getKind() == libsbml.UNIT_KIND_LITRE);
}
public void test_SBMLConvert_convertFromL3_priority()
{
SBMLDocument d = new SBMLDocument(3, 1);
Model m = d.createModel();
Event e = m.createEvent();
Priority p = e.createPriority();
assertTrue(d.setLevelAndVersion(1, 1, false) == false);
assertTrue(d.setLevelAndVersion(1, 2, false) == true);
assertTrue(d.setLevelAndVersion(2, 1, false) == true);
assertTrue(d.setLevelAndVersion(2, 2, false) == true);
assertTrue(d.setLevelAndVersion(2, 3, false) == true);
assertTrue(d.setLevelAndVersion(2, 4, false) == true);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
}
public void test_SBMLConvert_convertToL1_Species_Amount()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
string sid = "C";
Compartment c = new Compartment(2, 4);
Species s = new Species(2, 4);
c.setId(sid);
m.addCompartment(c);
s.setCompartment(sid);
s.setInitialAmount(2.34);
m.addSpecies(s);
assertTrue(d.setLevelAndVersion(1, 2, true) == true);
assertTrue(s.getInitialAmount() == 2.34);
d = null;
}
public void test_SBMLConvert_convertToL2v4_DuplicateAnnotations_model()
{
SBMLDocument d = new SBMLDocument(2, 1);
Model m = d.createModel();
string annotation = "<rdf/>\n<rdf/>";
int i = (m).setAnnotation(annotation);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
assertTrue((m).getAnnotation().getNumChildren() == 2);
assertTrue(d.setLevelAndVersion(2, 4, true) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 4);
m = d.getModel();
assertTrue((m).getAnnotation().getNumChildren() == 1);
d = null;
}
public void test_SBMLConvert_convertToL3_unit()
{
SBMLDocument d = new SBMLDocument(2, 2);
Model m = d.createModel();
string sid = "C";
UnitDefinition ud = m.createUnitDefinition();
ud.setId(sid);
Unit u = ud.createUnit();
u.setKind(libsbml.UNIT_KIND_MOLE);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
Unit u1 = m.getUnitDefinition(0).getUnit(0);
assertTrue(u1.hasRequiredAttributes() == true);
d = null;
}
public void test_SBMLConvert_convertFromL3_persistent()
{
SBMLDocument d = new SBMLDocument(3, 1);
Model m = d.createModel();
Event e = m.createEvent();
Trigger t = e.createTrigger();
t.setPersistent(false);
assertTrue(d.setLevelAndVersion(1, 1, false) == false);
assertTrue(d.setLevelAndVersion(1, 2, false) == true);
assertTrue(d.setLevelAndVersion(2, 1, false) == true);
assertTrue(d.setLevelAndVersion(2, 2, false) == true);
assertTrue(d.setLevelAndVersion(2, 3, false) == true);
assertTrue(d.setLevelAndVersion(2, 4, false) == true);
assertTrue(d.setLevelAndVersion(3, 1, false) == true);
}
/// <summary>
/// Converts a SBML document to the latest version (3.1) that is supported.
/// </summary>
private void convertSBML(SBMLDocument sbmlDoc)
{
var latestLevel = SBMLDocument.getDefaultLevel();
var latestVersion = SBMLDocument.getDefaultVersion();
if (sbmlDoc.getLevel() == latestLevel || sbmlDoc.getVersion() == latestVersion)
{
return;
}
var success = sbmlDoc.setLevelAndVersion(latestLevel, latestVersion);
if (!success)
{
throw new MoBiException(SBMLConstants.CouldNotConvertToActualLevel(latestLevel, latestVersion,
sbmlDoc.getLevel(), sbmlDoc.getVersion()));
}
}
public void test_SBMLConvert_addModifiersToReaction()
{
SBMLDocument d = new SBMLDocument(1, 2);
Model m = d.createModel();
Reaction r = m.createReaction();
KineticLaw kl = r.createKineticLaw();
kl.setFormula("k1*S1*S2*S3*S4*S5");
SimpleSpeciesReference ssr1;
SimpleSpeciesReference ssr2;
Species s1 = m.createSpecies();
s1.setId("S1");
Species s2 = m.createSpecies();
s2.setId("S2");
Species s3 = m.createSpecies();
s3.setId("S3");
Species s4 = m.createSpecies();
s4.setId("S4");
Species s5 = m.createSpecies();
s5.setId("S5");
SpeciesReference sr1 = r.createReactant();
SpeciesReference sr2 = r.createReactant();
SpeciesReference sr3 = r.createProduct();
sr1.setSpecies("S1");
sr2.setSpecies("S2");
sr3.setSpecies("S5");
assertTrue(r.getNumModifiers() == 0);
assertTrue(d.setLevelAndVersion(2, 1, false) == true);
assertTrue(d.getLevel() == 2);
assertTrue(d.getVersion() == 1);
assertTrue(m.getReaction(0).getNumModifiers() == 2);
ssr1 = m.getReaction(0).getModifier(0);
ssr2 = m.getReaction(0).getModifier(1);
assertTrue(("S3" == ssr1.getSpecies()));
assertTrue(("S4" == ssr2.getSpecies()));
d = null;
}
public void test_SBMLConvert_convertFromL3_conversionFactor()
{
SBMLDocument d = new SBMLDocument(3, 1);
Model m = d.createModel();
string sid = "P";
m.setConversionFactor(sid);
Parameter c = m.createParameter();
c.setId(sid);
c.setConstant(true);
assertTrue(d.setLevelAndVersion(1, 1, true) == false);
assertTrue(d.setLevelAndVersion(1, 2, true) == false);
assertTrue(d.setLevelAndVersion(2, 1, true) == false);
assertTrue(d.setLevelAndVersion(2, 2, true) == false);
assertTrue(d.setLevelAndVersion(2, 3, true) == false);
assertTrue(d.setLevelAndVersion(2, 4, true) == false);
assertTrue(d.setLevelAndVersion(3, 1, true) == true);
}