public void test_Event_addEventAssignment2()
{
Event e = new Event(2, 2);
EventAssignment ea = new EventAssignment(2, 3);
ea.setVariable("f");
ea.setMath(libsbml.parseFormula("a-n"));
int i = e.addEventAssignment(ea);
assertTrue(i == libsbml.LIBSBML_VERSION_MISMATCH);
assertTrue(e.getNumEventAssignments() == 0);
ea = null;
e = null;
}
public void test_EventAssignment_parent_add()
{
Event e = new Event(2, 4);
EventAssignment ea = new EventAssignment(2, 4);
ea.setVariable("c");
ea.setMath(libsbml.parseFormula("K+L"));
e.addEventAssignment(ea);
ea = null;
ListOf lo = e.getListOfEventAssignments();
assertTrue(lo == e.getEventAssignment(0).getParentSBMLObject());
assertTrue(e == lo.getParentSBMLObject());
}
printEventAssignmentMath(int n, EventAssignment ea)
{
string variable;
string formula;
if (ea.isSetMath())
{
variable = ea.getVariable();
formula = libsbml.formulaToString(ea.getMath());
Console.Write(" EventAssignment " + n
+ ", trigger: " + variable + " = " + formula + Environment.NewLine);
}
}
public void TestSerializationEventAssignment()
{
EventAssignment x1 = CreateObject <EventAssignment>().WithName("Eva").WithDimension(DimensionLength);
x1.ParentContainer = C0;
x1.UseAsValue = true;
x1.ObjectPath = ObjectPathFactory.CreateAbsoluteObjectPath(P);
x1.Formula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(23.4);
x1.ResolveChangedEntity();
IEventAssignment x2 = SerializeAndDeserialize(x1);
x2.ParentContainer = C0;
x2.ResolveChangedEntity();
AssertForSpecs.AreEqualEventAssignment(x2, x1);
}
public void test_Event_addEventAssignment1()
{
Event e = new Event(2, 2);
EventAssignment ea = new EventAssignment(2, 2);
int i = e.addEventAssignment(ea);
assertTrue(i == libsbml.LIBSBML_INVALID_OBJECT);
ea.setVariable("f");
i = e.addEventAssignment(ea);
assertTrue(i == libsbml.LIBSBML_INVALID_OBJECT);
ea.setMath(libsbml.parseFormula("a-n"));
i = e.addEventAssignment(ea);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(e.getNumEventAssignments() == 1);
ea = null;
e = null;
}
public void test_EventAssignment_ancestor_add()
{
Event e = new Event(2, 4);
EventAssignment ea = new EventAssignment(2, 4);
ea.setVariable("c");
ea.setMath(libsbml.parseFormula("K+L"));
e.addEventAssignment(ea);
ea = null;
ListOf lo = e.getListOfEventAssignments();
EventAssignment obj = e.getEventAssignment(0);
assertTrue(obj.getAncestorOfType(libsbml.SBML_EVENT) == e);
assertTrue(obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
}
public void test_EventAssignment_ancestor_create()
{
Event e = new Event(2, 4);
EventAssignment ea = e.createEventAssignment();
ListOf lo = e.getListOfEventAssignments();
assertTrue(ea.getAncestorOfType(libsbml.SBML_EVENT) == e);
assertTrue(ea.getAncestorOfType(libsbml.SBML_LIST_OF) == lo);
assertTrue(ea.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(ea.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
EventAssignment obj = e.getEventAssignment(0);
assertTrue(obj.getAncestorOfType(libsbml.SBML_EVENT) == e);
assertTrue(obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo);
assertTrue(obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null);
assertTrue(obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null);
}
public void test_EventAssignment_copyConstructor()
{
EventAssignment o1 = new EventAssignment(2, 4);
o1.setVariable("c2");
assertTrue(o1.getVariable() == "c2");
ASTNode node = new ASTNode(libsbml.AST_CONSTANT_PI);
o1.setMath(node);
node = null;
assertTrue(o1.getMath() != null);
EventAssignment o2 = new EventAssignment(o1);
assertTrue(o2.getVariable() == "c2");
assertTrue(o2.getMath() != null);
assertTrue(o2.getParentSBMLObject() == o1.getParentSBMLObject());
o2 = null;
o1 = null;
}
public void test_Event_full()
{
ASTNode math1 = libsbml.parseFormula("0");
Trigger trigger = new Trigger(2, 4);
ASTNode math = libsbml.parseFormula("0");
Event e = new Event(2, 4);
EventAssignment ea = new EventAssignment(2, 4);
ea.setVariable("k");
ea.setMath(math);
trigger.setMath(math1);
e.setTrigger(trigger);
e.setId("e1");
e.setName("Set k2 to zero when P1 <= t");
e.addEventAssignment(ea);
assertTrue(e.getNumEventAssignments() == 1);
assertNotEquals(e.getEventAssignment(0), ea);
math = null;
e = null;
}
public void test_EventAssignment_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2, 1);
sbmlns.addNamespaces(xmlns);
EventAssignment object1 = new EventAssignment(sbmlns);
assertTrue(object1.getTypeCode() == libsbml.SBML_EVENT_ASSIGNMENT);
assertTrue(object1.getMetaId() == "");
assertTrue(object1.getNotes() == null);
assertTrue(object1.getAnnotation() == null);
assertTrue(object1.getLevel() == 2);
assertTrue(object1.getVersion() == 1);
assertTrue(object1.getNamespaces() != null);
assertTrue(object1.getNamespaces().getLength() == 2);
object1 = null;
}
public void test_Event_parent_NULL()
{
SBMLDocument d = new SBMLDocument(2, 4);
Model m = d.createModel();
Event c = m.createEvent();
EventAssignment ea = c.createEventAssignment();
Trigger t = new Trigger(2, 4);
t.setMath(new ASTNode());
Delay dy = new Delay(2, 4);
dy.setMath(new ASTNode());
c.setTrigger(t);
c.setDelay(dy);
assertTrue(c.getAncestorOfType(libsbml.SBML_MODEL) == m);
assertTrue(c.getTrigger().getParentSBMLObject() == c);
assertEquals(c.getDelay().getSBMLDocument(), d);
assertTrue(ea.getAncestorOfType(libsbml.SBML_EVENT) == c);
Event c1 = c.clone();
d = null;
assertTrue(c1.getAncestorOfType(libsbml.SBML_MODEL) == null);
assertTrue(c1.getParentSBMLObject() == null);
assertEquals(c1.getSBMLDocument(), null);
assertTrue(c1.getEventAssignment(0).getAncestorOfType(libsbml.SBML_MODEL) == null);
assertTrue(c1.getEventAssignment(0).getAncestorOfType(libsbml.SBML_EVENT) == c1);
assertTrue(c1.getEventAssignment(0).getParentSBMLObject() != null);
assertEquals(c1.getEventAssignment(0).getSBMLDocument(), null);
assertTrue(c1.getTrigger().getAncestorOfType(libsbml.SBML_MODEL) == null);
assertTrue(c1.getTrigger().getAncestorOfType(libsbml.SBML_EVENT) == c1);
assertTrue(c1.getTrigger().getParentSBMLObject() != null);
assertEquals(c1.getTrigger().getSBMLDocument(), null);
assertTrue(c1.getDelay().getAncestorOfType(libsbml.SBML_MODEL) == null);
assertTrue(c1.getDelay().getAncestorOfType(libsbml.SBML_EVENT) == c1);
assertTrue(c1.getDelay().getParentSBMLObject() != null);
assertEquals(c1.getDelay().getSBMLDocument(), null);
c1 = null;
}
static void testListOfRemove(ListOf lof, SBase s)
{
string ename = s.getElementName();
lof.append(s);
SBase c = lof.get(0);
if (c is CompartmentType)
{
CompartmentType x = (lof as ListOfCompartmentTypes).remove(0); c = x;
}
else if (c is Compartment)
{
Compartment x = (lof as ListOfCompartments).remove(0); c = x;
}
else if (c is Constraint)
{
Constraint x = (lof as ListOfConstraints).remove(0); c = x;
}
else if (c is EventAssignment)
{
EventAssignment x = (lof as ListOfEventAssignments).remove(0); c = x;
}
else if (c is Event)
{
Event x = (lof as ListOfEvents).remove(0); c = x;
}
else if (c is FunctionDefinition)
{
FunctionDefinition x = (lof as ListOfFunctionDefinitions).remove(0); c = x;
}
else if (c is InitialAssignment)
{
InitialAssignment x = (lof as ListOfInitialAssignments).remove(0); c = x;
}
else if (c is Parameter)
{
Parameter x = (lof as ListOfParameters).remove(0); c = x;
}
else if (c is Reaction)
{
Reaction x = (lof as ListOfReactions).remove(0); c = x;
}
else if (c is Rule)
{
Rule x = (lof as ListOfRules).remove(0); c = x;
}
else if (c is Species)
{
Species x = (lof as ListOfSpecies).remove(0); c = x;
}
else if (c is SpeciesReference)
{
SimpleSpeciesReference x = (lof as ListOfSpeciesReferences).remove(0); c = x;
}
else if (c is SpeciesType)
{
SpeciesType x = (lof as ListOfSpeciesTypes).remove(0); c = x;
}
else if (c is UnitDefinition)
{
UnitDefinition x = (lof as ListOfUnitDefinitions).remove(0); c = x;
}
else if (c is Unit)
{
Unit x = (lof as ListOfUnits).remove(0); c = x;
}
else
{
ERR("[testListOfRemove] Error: (" + ename + ") : ListOfXXX::remove() failed.");
return;
}
if (c == null)
{
ERR("[testListOfRemove] Error: (" + ename + ") : ListOfXXX::remove() failed.");
return;
}
string enameGet = c.getElementName();
if (ename == enameGet)
{
//Console.Out.WriteLine("[testListOfRemove] OK: (" + ename + ") remove(" + enameGet + ") : type match.");
OK();
}
else
{
ERR("[testListOfRemove] Error: (" + ename + ") remove(" + enameGet + ") : type mismatch.");
}
}
static void testClone(SBase s)
{
string ename = s.getElementName();
SBase c = s.clone();
if (c is Compartment)
{
Compartment x = (s as Compartment).clone(); c = x;
}
else if (c is CompartmentType)
{
CompartmentType x = (s as CompartmentType).clone(); c = x;
}
else if (c is Constraint)
{
Constraint x = (s as Constraint).clone(); c = x;
}
else if (c is Delay)
{
Delay x = (s as Delay).clone(); c = x;
}
else if (c is Event)
{
Event x = (s as Event).clone(); c = x;
}
else if (c is EventAssignment)
{
EventAssignment x = (s as EventAssignment).clone(); c = x;
}
else if (c is FunctionDefinition)
{
FunctionDefinition x = (s as FunctionDefinition).clone(); c = x;
}
else if (c is InitialAssignment)
{
InitialAssignment x = (s as InitialAssignment).clone(); c = x;
}
else if (c is KineticLaw)
{
KineticLaw x = (s as KineticLaw).clone(); c = x;
}
// currently return type of ListOf::clone() is SBase
else if (c is ListOf)
{
SBase x = (s as ListOf).clone(); c = x;
}
else if (c is Model)
{
Model x = (s as Model).clone(); c = x;
}
else if (c is Parameter)
{
Parameter x = (s as Parameter).clone(); c = x;
}
else if (c is Reaction)
{
Reaction x = (s as Reaction).clone(); c = x;
}
else if (c is AlgebraicRule)
{
AlgebraicRule x = (s as AlgebraicRule).clone(); c = x;
}
else if (c is AssignmentRule)
{
AssignmentRule x = (s as AssignmentRule).clone(); c = x;
}
else if (c is RateRule)
{
RateRule x = (s as RateRule).clone(); c = x;
}
else if (c is SBMLDocument)
{
SBMLDocument x = (s as SBMLDocument).clone(); c = x;
}
else if (c is Species)
{
Species x = (s as Species).clone(); c = x;
}
else if (c is SpeciesReference)
{
SpeciesReference x = (s as SpeciesReference).clone(); c = x;
}
else if (c is SpeciesType)
{
SpeciesType x = (s as SpeciesType).clone(); c = x;
}
else if (c is SpeciesReference)
{
SpeciesReference x = (s as SpeciesReference).clone(); c = x;
}
else if (c is StoichiometryMath)
{
StoichiometryMath x = (s as StoichiometryMath).clone(); c = x;
}
else if (c is Trigger)
{
Trigger x = (s as Trigger).clone(); c = x;
}
else if (c is Unit)
{
Unit x = (s as Unit).clone(); c = x;
}
else if (c is UnitDefinition)
{
UnitDefinition x = (s as UnitDefinition).clone(); c = x;
}
else if (c is ListOfCompartmentTypes)
{
ListOfCompartmentTypes x = (s as ListOfCompartmentTypes).clone(); c = x;
}
else if (c is ListOfCompartments)
{
ListOfCompartments x = (s as ListOfCompartments).clone(); c = x;
}
else if (c is ListOfConstraints)
{
ListOfConstraints x = (s as ListOfConstraints).clone(); c = x;
}
else if (c is ListOfEventAssignments)
{
ListOfEventAssignments x = (s as ListOfEventAssignments).clone(); c = x;
}
else if (c is ListOfEvents)
{
ListOfEvents x = (s as ListOfEvents).clone(); c = x;
}
else if (c is ListOfFunctionDefinitions)
{
ListOfFunctionDefinitions x = (s as ListOfFunctionDefinitions).clone(); c = x;
}
else if (c is ListOfInitialAssignments)
{
ListOfInitialAssignments x = (s as ListOfInitialAssignments).clone(); c = x;
}
else if (c is ListOfParameters)
{
ListOfParameters x = (s as ListOfParameters).clone(); c = x;
}
else if (c is ListOfReactions)
{
ListOfReactions x = (s as ListOfReactions).clone(); c = x;
}
else if (c is ListOfRules)
{
ListOfRules x = (s as ListOfRules).clone(); c = x;
}
else if (c is ListOfSpecies)
{
ListOfSpecies x = (s as ListOfSpecies).clone(); c = x;
}
else if (c is ListOfSpeciesReferences)
{
ListOfSpeciesReferences x = (s as ListOfSpeciesReferences).clone(); c = x;
}
else if (c is ListOfSpeciesTypes)
{
ListOfSpeciesTypes x = (s as ListOfSpeciesTypes).clone(); c = x;
}
else if (c is ListOfUnitDefinitions)
{
ListOfUnitDefinitions x = (s as ListOfUnitDefinitions).clone(); c = x;
}
else if (c is ListOfUnits)
{
ListOfUnits x = (s as ListOfUnits).clone(); c = x;
}
else
{
ERR("[testClone] Error: (" + ename + ") : clone() failed.");
return;
}
if (c == null)
{
ERR("[testClone] Error: (" + ename + ") : clone() failed.");
return;
}
string enameClone = c.getElementName();
if (ename == enameClone)
{
//Console.Out.WriteLine("[testClone] OK: (" + ename + ") clone(" + enameClone + ") : type match.");
OK();
}
else
{
ERR("[testClone] Error: (" + ename + ") clone(" + enameClone + ") : type mismatch.");
}
}
public static int Main(string[] args)
{
if (args.Length != 1)
{
Console.WriteLine("Usage: printUnits filename");
return(1);
}
string filename = args[0];
SBMLDocument document = libsbml.readSBML(filename);
if (document.getNumErrors() > 0)
{
Console.Error.WriteLine("Encountered the following SBML errors:");
document.printErrors();
return(1);
}
Model model = document.getModel();
if (model == null)
{
Console.WriteLine("No model present.");
return(1);
}
int i, j;
for (i = 0; i < model.getNumSpecies(); i++)
{
Species s = model.getSpecies(i);
Console.WriteLine("Species " + i + ": "
+ UnitDefinition.printUnits(s.getDerivedUnitDefinition()));
}
for (i = 0; i < model.getNumCompartments(); i++)
{
Compartment c = model.getCompartment(i);
Console.WriteLine("Compartment " + i + ": "
+ UnitDefinition.printUnits(c.getDerivedUnitDefinition()))
;
}
for (i = 0; i < model.getNumParameters(); i++)
{
Parameter p = model.getParameter(i);
Console.WriteLine("Parameter " + i + ": "
+ UnitDefinition.printUnits(p.getDerivedUnitDefinition()))
;
}
for (i = 0; i < model.getNumInitialAssignments(); i++)
{
InitialAssignment ia = model.getInitialAssignment(i);
Console.WriteLine("InitialAssignment " + i + ": "
+ UnitDefinition.printUnits(ia.getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((ia.containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
for (i = 0; i < model.getNumEvents(); i++)
{
Event e = model.getEvent(i);
Console.WriteLine("Event " + i + ": ");
if (e.isSetDelay())
{
Console.WriteLine("Delay: "
+ UnitDefinition.printUnits(e.getDelay().getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((e.getDelay().containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
for (j = 0; j < e.getNumEventAssignments(); j++)
{
EventAssignment ea = e.getEventAssignment(j);
Console.WriteLine("EventAssignment " + j + ": "
+ UnitDefinition.printUnits(ea.getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((ea.containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
}
for (i = 0; i < model.getNumReactions(); i++)
{
Reaction r = model.getReaction(i);
Console.WriteLine("Reaction " + i + ": ");
if (r.isSetKineticLaw())
{
Console.WriteLine("Kinetic Law: "
+ UnitDefinition.printUnits(r.getKineticLaw().getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((r.getKineticLaw().containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
for (j = 0; j < r.getNumReactants(); j++)
{
SpeciesReference sr = r.getReactant(j);
if (sr.isSetStoichiometryMath())
{
Console.WriteLine("Reactant stoichiometryMath" + j + ": "
+ UnitDefinition.printUnits(sr.getStoichiometryMath().getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((sr.getStoichiometryMath().containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
}
for (j = 0; j < r.getNumProducts(); j++)
{
SpeciesReference sr = r.getProduct(j);
if (sr.isSetStoichiometryMath())
{
Console.WriteLine("Product stoichiometryMath" + j + ": "
+ UnitDefinition.printUnits(sr.getStoichiometryMath().getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((sr.getStoichiometryMath().containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
}
}
for (i = 0; i < model.getNumRules(); i++)
{
Rule r = model.getRule(i);
Console.WriteLine("Rule " + i + ": "
+ UnitDefinition.printUnits(r.getDerivedUnitDefinition()));
Console.WriteLine(" undeclared units: ");
Console.WriteLine((r.containsUndeclaredUnits() ? "yes\n" : "no\n"));
}
return(0);
}
public static int Main(string[] args)
{
if (args.Length != 1)
{
Console.WriteLine("Usage: printNotes filename");
return(1);
}
int i, j;
string filename = args[0];
SBMLDocument document;
document = libsbml.readSBML(filename);
int errors = (int)document.getNumErrors();
Console.WriteLine();
Console.WriteLine("filename: " + filename);
Console.WriteLine();
if (errors > 0)
{
document.printErrors();
return(errors);
}
/* Model */
Model m = document.getModel();
printNotes(m);
for (i = 0; i < m.getNumReactions(); i++)
{
Reaction re = m.getReaction(i);
printNotes(re);
/* SpeciesReference (Reacatant) */
for (j = 0; j < re.getNumReactants(); j++)
{
SpeciesReference rt = re.getReactant(j);
if (rt.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(rt, (rt.isSetSpecies() ? rt.getSpecies() : ""));
}
/* SpeciesReference (Product) */
for (j = 0; j < re.getNumProducts(); j++)
{
SpeciesReference rt = re.getProduct(j);
if (rt.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(rt, (rt.isSetSpecies() ? rt.getSpecies() : ""));
}
/* ModifierSpeciesReference (Modifier) */
for (j = 0; j < re.getNumModifiers(); j++)
{
ModifierSpeciesReference md = re.getModifier(j);
if (md.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(md, (md.isSetSpecies() ? md.getSpecies() : ""));
}
/* Kineticlaw */
if (re.isSetKineticLaw())
{
KineticLaw kl = re.getKineticLaw();
if (kl.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(kl);
/* Parameter */
for (j = 0; j < kl.getNumParameters(); j++)
{
Parameter pa = kl.getParameter(j);
if (pa.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(pa);
}
}
}
/* Species */
for (i = 0; i < m.getNumSpecies(); i++)
{
Species sp = m.getSpecies(i);
printNotes(sp);
}
/* Compartment */
for (i = 0; i < m.getNumCompartments(); i++)
{
Compartment sp = m.getCompartment(i);
printNotes(sp);
}
/* FunctionDefinition */
for (i = 0; i < m.getNumFunctionDefinitions(); i++)
{
FunctionDefinition sp = m.getFunctionDefinition(i);
printNotes(sp);
}
/* UnitDefinition */
for (i = 0; i < m.getNumUnitDefinitions(); i++)
{
UnitDefinition sp = m.getUnitDefinition(i);
printNotes(sp);
}
/* Parameter */
for (i = 0; i < m.getNumParameters(); i++)
{
Parameter sp = m.getParameter(i);
printNotes(sp);
}
/* Rule */
for (i = 0; i < m.getNumRules(); i++)
{
Rule sp = m.getRule(i);
printNotes(sp);
}
/* InitialAssignment */
for (i = 0; i < m.getNumInitialAssignments(); i++)
{
InitialAssignment sp = m.getInitialAssignment(i);
printNotes(sp);
}
/* Event */
for (i = 0; i < m.getNumEvents(); i++)
{
Event sp = m.getEvent(i);
printNotes(sp);
/* Trigger */
if (sp.isSetTrigger())
{
Trigger tg = sp.getTrigger();
if (tg.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(tg);
}
/* Delay */
if (sp.isSetDelay())
{
Delay dl = sp.getDelay();
if (dl.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(dl);
}
/* EventAssignment */
for (j = 0; j < sp.getNumEventAssignments(); j++)
{
EventAssignment ea = sp.getEventAssignment(j);
if (ea.isSetNotes())
{
Console.WriteLine(" ");
}
printNotes(ea);
}
}
/* SpeciesType */
for (i = 0; i < m.getNumSpeciesTypes(); i++)
{
SpeciesType sp = m.getSpeciesType(i);
printNotes(sp);
}
/* Constraint */
for (i = 0; i < m.getNumConstraints(); i++)
{
Constraint sp = m.getConstraint(i);
printNotes(sp);
}
return(errors);
}
public static int Main(string[] args)
{
if (args.Length != 2)
{
Console.Write(Environment.NewLine + "Usage: unsetAnnotation <input-filename> <output-filename>" + Environment.NewLine + Environment.NewLine);
return 1;
}
int i, j;
string filename = args[0];
SBMLDocument document;
document = libsbml.readSBML(filename);
int errors = (int)document.getNumErrors();
if (errors > 0)
{
document.printErrors();
return errors;
}
Model m = document.getModel();
m.unsetAnnotation();
for (i = 0; i < m.getNumReactions(); i++)
{
Reaction re = m.getReaction(i);
re.unsetAnnotation();
for (j = 0; j < re.getNumReactants(); j++)
{
SpeciesReference rt = re.getReactant(j);
rt.unsetAnnotation();
}
for (j = 0; j < re.getNumProducts(); j++)
{
SpeciesReference rt = re.getProduct(j);
rt.unsetAnnotation();
}
for (j = 0; j < re.getNumModifiers(); j++)
{
ModifierSpeciesReference md = re.getModifier(j);
md.unsetAnnotation();
}
if (re.isSetKineticLaw())
{
KineticLaw kl = re.getKineticLaw();
kl.unsetAnnotation();
for (j = 0; j < kl.getNumParameters(); j++)
{
Parameter pa = kl.getParameter(j);
pa.unsetAnnotation();
}
}
}
for (i = 0; i < m.getNumSpecies(); i++)
{
Species sp = m.getSpecies(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumCompartments(); i++)
{
Compartment sp = m.getCompartment(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumFunctionDefinitions(); i++)
{
FunctionDefinition sp = m.getFunctionDefinition(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumUnitDefinitions(); i++)
{
UnitDefinition sp = m.getUnitDefinition(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumParameters(); i++)
{
Parameter sp = m.getParameter(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumRules(); i++)
{
Rule sp = m.getRule(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumInitialAssignments(); i++)
{
InitialAssignment sp = m.getInitialAssignment(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumEvents(); i++)
{
Event sp = m.getEvent(i);
sp.unsetAnnotation();
for (j = 0; j < sp.getNumEventAssignments(); j++)
{
EventAssignment ea = sp.getEventAssignment(j);
ea.unsetAnnotation();
}
}
for (i = 0; i < m.getNumSpeciesTypes(); i++)
{
SpeciesType sp = m.getSpeciesType(i);
sp.unsetAnnotation();
}
for (i = 0; i < m.getNumConstraints(); i++)
{
Constraint sp = m.getConstraint(i);
sp.unsetAnnotation();
}
libsbml.writeSBML(document, args[1]);
return errors;
}
public void EventAssignmentElement(Hashtable attrs)
{
String variable;
SBase parameter = null;
if (attrs.Contains("variable"))
{
variable = (String)attrs["variable"];
if (this.model.findObject(variable) != null)
parameter = (SBase)this.model.findObject(variable);
}
EventAssignment eventAssignment = new EventAssignment(this.model, parameter);
Event eventNode = (Event)elementStack.Peek();
eventNode.listOfEventAssignments.Add(eventAssignment);
elementStack.Push(eventAssignment);
}
public static void Initialize(SchoolContext context)
{
//context.Database.EnsureCreated();
// Look for any Athletes.
if (context.Athletes.Any())
{
return; // DB has been seeded
}
var Athletes = new Athlete[]
{
new Athlete {
FirstName = "Carson", LastName = "Alexander", Gender = Gender.Male, Dob = DateTime.Parse("1995-05-30"), Weight = 140, Height = 50
},
new Athlete {
FirstName = "Meredith", LastName = "Alonso", Gender = Gender.Male, Dob = DateTime.Parse("1992-07-5"), Weight = 160, Height = 60
},
new Athlete {
FirstName = "Arturo", LastName = "Anand", Gender = Gender.Male, Dob = DateTime.Parse("1993-02-15"), Weight = 165, Height = 55
},
new Athlete {
FirstName = "Gytis", LastName = "JELLISON", Gender = Gender.Female, Dob = DateTime.Parse("1992-02-27"), Weight = 125, Height = 47
},
new Athlete {
FirstName = "Yan", MiddleName = "Lee", LastName = "Li", Gender = Gender.Male, Dob = DateTime.Parse("1992-08-24"), Weight = 140, Height = 73
},
new Athlete {
FirstName = "Peggy", MiddleName = "Laura", LastName = "Justice", Gender = Gender.Female, Dob = DateTime.Parse("1991-08-03"), Weight = 230, Height = 73
},
new Athlete {
FirstName = "Laura", MiddleName = "Nicole", LastName = "Norman", Gender = Gender.Female, Dob = DateTime.Parse("1993-04-03"), Weight = 135, Height = 67
},
new Athlete {
FirstName = "Tom", MiddleName = "Marvolo", LastName = "Riddle", Gender = Gender.Male, Dob = DateTime.Parse("1995-04-11"), Weight = 145, Height = 76
},
new Athlete {
FirstName = "Carl", LastName = "Gibbons", Gender = Gender.Male, Dob = DateTime.Parse("1969-05-30"), Weight = 212, Height = 70
},
new Athlete {
FirstName = "Jackson ", LastName = "Smith ", Gender = Gender.Male, Dob = DateTime.Parse("1995-05-30"), Weight = 140, Height = 50
},
new Athlete {
FirstName = "Sebastian ", LastName = "Smith ", Gender = Gender.Male, Dob = DateTime.Parse("1992-07-5"), Weight = 160, Height = 60
},
new Athlete {
FirstName = "Aiden ", LastName = "Smith ", Gender = Gender.Male, Dob = DateTime.Parse("1991-02-15"), Weight = 165, Height = 55
},
new Athlete {
FirstName = "Matthew ", LastName = "Smith ", Gender = Gender.Female, Dob = DateTime.Parse("1992-02-20"), Weight = 125, Height = 47
},
new Athlete {
FirstName = "Samuel ", MiddleName = "Colt ", LastName = "CarolsunlutzenBurhSchmity", Gender = Gender.Male, Dob = DateTime.Parse("1992-08-29"), Weight = 140, Height = 73
},
new Athlete {
FirstName = "David ", MiddleName = "Archer ", LastName = "Wheat", Gender = Gender.Female, Dob = DateTime.Parse("1998-08-03"), Weight = 230, Height = 73
},
new Athlete {
FirstName = "Joseph ", MiddleName = "Omar ", LastName = "Desk", Gender = Gender.Female, Dob = DateTime.Parse("1997-04-03"), Weight = 135, Height = 67
},
new Athlete {
FirstName = "Tom", MiddleName = "Aidan ", LastName = "Oliveoil", Gender = Gender.Male, Dob = DateTime.Parse("1995-04-11"), Weight = 145, Height = 76
},
new Athlete {
FirstName = "Carter ", LastName = "Gibbons", Gender = Gender.Male, Dob = DateTime.Parse("1969-05-30"), Weight = 212, Height = 70
},
new Athlete {
FirstName = "Harper", LastName = "WhiteHouse", Gender = Gender.Male, Dob = DateTime.Parse("1995-05-30"), Weight = 140, Height = 50
},
new Athlete {
FirstName = "Meredith", LastName = "Ammoury", Gender = Gender.Male, Dob = DateTime.Parse("1992-07-5"), Weight = 160, Height = 60
},
new Athlete {
FirstName = "Evelyn", LastName = "Swartzburg", Gender = Gender.Male, Dob = DateTime.Parse("1993-02-13"), Weight = 165, Height = 55
},
new Athlete {
FirstName = "Abigail", LastName = "Disndy", Gender = Gender.Female, Dob = DateTime.Parse("1992-02-17"), Weight = 125, Height = 47
},
new Athlete {
FirstName = "Emily", MiddleName = "Ememin", LastName = "Li", Gender = Gender.Male, Dob = DateTime.Parse("1992-08-21"), Weight = 140, Height = 73
},
new Athlete {
FirstName = "Elizabeth", LastName = "Kalifia", Gender = Gender.Female, Dob = DateTime.Parse("1991-08-03"), Weight = 230, Height = 73
},
new Athlete {
FirstName = "Mila", LastName = "Prettyman", Gender = Gender.Female, Dob = DateTime.Parse("1993-04-23"), Weight = 135, Height = 67
},
new Athlete {
FirstName = "Ella", LastName = "Larson", Gender = Gender.Male, Dob = DateTime.Parse("1995-04-22"), Weight = 145, Height = 76
},
new Athlete {
FirstName = "Avery", LastName = "Thayne", Gender = Gender.Male, Dob = DateTime.Parse("1969-05-02"), Weight = 212, Height = 70
},
new Athlete {
FirstName = "Riley", LastName = "Ocean", Gender = Gender.Male, Dob = DateTime.Parse("1995-05-03"), Weight = 140, Height = 50
},
new Athlete {
FirstName = "Nora", LastName = "Excalaber", Gender = Gender.Male, Dob = DateTime.Parse("1992-07-15"), Weight = 160, Height = 60
},
new Athlete {
FirstName = "Eleanor", LastName = "Ansley", Gender = Gender.Male, Dob = DateTime.Parse("1993-02-15"), Weight = 165, Height = 55
},
new Athlete {
FirstName = "Hannah", LastName = "Barzee", Gender = Gender.Female, Dob = DateTime.Parse("1992-02-26"), Weight = 125, Height = 47
},
new Athlete {
FirstName = "Mason ", MiddleName = "Bryson ", LastName = "Li", Gender = Gender.Male, Dob = DateTime.Parse("1992-08-14"), Weight = 167, Height = 72
},
new Athlete {
FirstName = "Damian ", MiddleName = "Sawyer ", LastName = "Jenson", Gender = Gender.Female, Dob = DateTime.Parse("1991-08-05"), Weight = 213, Height = 73
},
new Athlete {
FirstName = "Silas ", MiddleName = "Nicole", LastName = "Raia", Gender = Gender.Female, Dob = DateTime.Parse("1993-04-03"), Weight = 189, Height = 78
},
new Athlete {
FirstName = "Chase ", MiddleName = "Declan ", LastName = "Riddle", Gender = Gender.Male, Dob = DateTime.Parse("1995-04-11"), Weight = 202, Height = 76
},
new Athlete {
FirstName = "Carl ", LastName = "Gibbons", Gender = Gender.Male, Dob = DateTime.Parse("1969-05-30"), Weight = 200, Height = 70
}
};
foreach (Athlete s in Athletes)
{
context.Athletes.Add(s);
}
context.SaveChanges();
var Coachs = new Coach[]
{
new Coach {
FirstName = "Kim", MiddleName = "Amber", LastName = "Abercrombie", HireDate = DateTime.Parse("1995-03-11")
},
new Coach {
FirstName = "Fadi", MiddleName = "Aliku", LastName = "Fakhouri", HireDate = DateTime.Parse("2002-07-06")
},
new Coach {
FirstName = "Tim", LastName = "Thayne", HireDate = DateTime.Parse("1998-07-01")
},
new Coach {
FirstName = "Candace", LastName = "Kapoor", HireDate = DateTime.Parse("2001-01-15")
},
new Coach {
FirstName = "Roger", LastName = "Zheng", HireDate = DateTime.Parse("2004-02-12")
}
};
foreach (Coach i in Coachs)
{
context.Coaches.Add(i);
}
context.SaveChanges();
var Fields = new Field[]
{
new Field {
Name = "Running", Budget = 357000,
StartDate = DateTime.Parse("2007-09-01"),
CoachID = Coachs.Single(i => i.LastName == "Thayne").ID
},
new Field {
Name = "Throwing", Budget = 0909000,
StartDate = DateTime.Parse("2007-09-01"),
CoachID = Coachs.Single(i => i.LastName == "Fakhouri").ID
},
new Field {
Name = "Jumping", Budget = 250000,
StartDate = DateTime.Parse("2007-09-01"),
CoachID = Coachs.Single(i => i.LastName == "Thayne").ID
}
};
foreach (Field d in Fields)
{
context.Fields.Add(d);
}
context.SaveChanges();
var Events = new Event[]
{
new Event {
EventID = 1001, Title = "100 Meters", FieldID = Fields.Single(s => s.Name == "Running").FieldID
},
new Event {
EventID = 1002, Title = "200 Meters", FieldID = Fields.Single(s => s.Name == "Running").FieldID
},
new Event {
EventID = 1003, Title = "400 Meters", FieldID = Fields.Single(s => s.Name == "Running").FieldID
},
new Event {
EventID = 1004, Title = "1500 Meters", FieldID = Fields.Single(s => s.Name == "Running").FieldID
},
new Event {
EventID = 1005, Title = "3000 Meters", FieldID = Fields.Single(s => s.Name == "Running").FieldID
},
new Event {
EventID = 1006, Title = "400 Meters", FieldID = Fields.Single(s => s.Name == "Running").FieldID
},
new Event {
EventID = 1007, Title = "100 Meter Hurdles", FieldID = Fields.Single(s => s.Name == "Running").FieldID
},
new Event {
EventID = 1008, Title = "400 Meters Hurdles", FieldID = Fields.Single(s => s.Name == "Running").FieldID
},
new Event {
EventID = 1009, Title = "4X100 Meter Relay", FieldID = Fields.Single(s => s.Name == "Running").FieldID
},
new Event {
EventID = 1010, Title = "4X400 Meters Relay", FieldID = Fields.Single(s => s.Name == "Running").FieldID
},
new Event {
EventID = 2001, Title = "High Jump", FieldID = Fields.Single(s => s.Name == "Jumping").FieldID
},
new Event {
EventID = 2002, Title = "Pole Vault", FieldID = Fields.Single(s => s.Name == "Jumping").FieldID
},
new Event {
EventID = 2003, Title = "Triple Jump", FieldID = Fields.Single(s => s.Name == "Jumping").FieldID
},
new Event {
EventID = 3001, Title = "Discus Throw", FieldID = Fields.Single(s => s.Name == "Throwing").FieldID
},
new Event {
EventID = 3002, Title = "Hammer Throw", FieldID = Fields.Single(s => s.Name == "Throwing").FieldID
},
new Event {
EventID = 3003, Title = "Shot Put", FieldID = Fields.Single(s => s.Name == "Throwing").FieldID
},
new Event {
EventID = 3004, Title = "Javelin Throw", FieldID = Fields.Single(s => s.Name == "Throwing").FieldID
}
};
foreach (Event c in Events)
{
context.Events.Add(c);
}
context.SaveChanges();
var EventCoach = new EventAssignment[]
{
new EventAssignment {
EventID = Events.Single(c => c.Title == "100 Meters").EventID,
CoachID = Coachs.Single(i => i.LastName == "Kapoor").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "200 Meters").EventID,
CoachID = Coachs.Single(i => i.LastName == "Kapoor").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "400 Meters").EventID,
CoachID = Coachs.Single(i => i.LastName == "Kapoor").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "1500 Meters").EventID,
CoachID = Coachs.Single(i => i.LastName == "Abercrombie").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "3000 Meters").EventID,
CoachID = Coachs.Single(i => i.LastName == "Abercrombie").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "100 Meter Hurdles").EventID,
CoachID = Coachs.Single(i => i.LastName == "Zheng").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "400 Meters Hurdles").EventID,
CoachID = Coachs.Single(i => i.LastName == "Zheng").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "4X100 Meter Relay").EventID,
CoachID = Coachs.Single(i => i.LastName == "Zheng").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "4X400 Meter Relay").EventID,
CoachID = Coachs.Single(i => i.LastName == "Zheng").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "High Jump").EventID,
CoachID = Coachs.Single(i => i.LastName == "Fakhouri").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "Pole Vault").EventID,
CoachID = Coachs.Single(i => i.LastName == "Fakhouri").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "Triple Jump").EventID,
CoachID = Coachs.Single(i => i.LastName == "Fakhouri").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "Discus Throw").EventID,
CoachID = Coachs.Single(i => i.LastName == "Thayne").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "Hammer Throw").EventID,
CoachID = Coachs.Single(i => i.LastName == "Thayne").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "Shot Put").EventID,
CoachID = Coachs.Single(i => i.LastName == "Thayne").ID
},
new EventAssignment {
EventID = Events.Single(c => c.Title == "Javelin Throw").EventID,
CoachID = Coachs.Single(i => i.LastName == "Thayne").ID
}
};
foreach (EventAssignment ci in EventCoach)
{
context.EventAssignments.Add(ci);
}
context.SaveChanges();
var trials = new Trial[]
{
//first
new Trial {
AthleteID = 35, EventID = 1001, Place = Place.First
},
new Trial {
AthleteID = 35, EventID = 1002, Place = Place.First
},
new Trial {
AthleteID = 35, EventID = 1003, Place = Place.First
},
new Trial {
AthleteID = 33, EventID = 1004, Place = Place.First
},
new Trial {
AthleteID = 5, EventID = 1005, Place = Place.First
},
new Trial {
AthleteID = 24, EventID = 1006, Place = Place.First
},
new Trial {
AthleteID = 13, EventID = 1007, Place = Place.First
},
new Trial {
AthleteID = 23, EventID = 1008, Place = Place.First
},
new Trial {
AthleteID = 14, EventID = 1009, Place = Place.First
},
new Trial {
AthleteID = 13, EventID = 1010, Place = Place.First
},
new Trial {
AthleteID = 10, EventID = 2001, Place = Place.First
},
new Trial {
AthleteID = 31, EventID = 2002, Place = Place.First
},
new Trial {
AthleteID = 27, EventID = 2003, Place = Place.First
},
new Trial {
AthleteID = 9, EventID = 3001, Place = Place.First
},
new Trial {
AthleteID = 5, EventID = 3002, Place = Place.First
},
new Trial {
AthleteID = 7, EventID = 3003, Place = Place.First
},
new Trial {
AthleteID = 16, EventID = 3004, Place = Place.First
},
new Trial {
AthleteID = 35, EventID = 1001, Place = Place.Second
},
new Trial {
AthleteID = 35, EventID = 1002, Place = Place.Second
},
new Trial {
AthleteID = 35, EventID = 1003, Place = Place.Second
},
new Trial {
AthleteID = 35, EventID = 1004, Place = Place.Second
},
new Trial {
AthleteID = 35, EventID = 1005, Place = Place.Second
},
new Trial {
AthleteID = 24, EventID = 1006, Place = Place.Second
},
new Trial {
AthleteID = 8, EventID = 1007, Place = Place.Second
},
new Trial {
AthleteID = 33, EventID = 1008, Place = Place.Second
},
new Trial {
AthleteID = 12, EventID = 1009, Place = Place.Second
},
new Trial {
AthleteID = 10, EventID = 1010, Place = Place.Second
},
new Trial {
AthleteID = 11, EventID = 2001, Place = Place.Second
},
new Trial {
AthleteID = 12, EventID = 2002, Place = Place.Second
},
new Trial {
AthleteID = 13, EventID = 2003, Place = Place.Second
},
new Trial {
AthleteID = 14, EventID = 3001, Place = Place.Second
},
new Trial {
AthleteID = 15, EventID = 3002, Place = Place.Second
},
new Trial {
AthleteID = 16, EventID = 3003, Place = Place.Second
},
new Trial {
AthleteID = 16, EventID = 3004, Place = Place.Second
},
new Trial {
AthleteID = 35, EventID = 1001, Place = Place.Third
},
new Trial {
AthleteID = 35, EventID = 1002, Place = Place.Third
},
new Trial {
AthleteID = 35, EventID = 1003, Place = Place.Third
},
new Trial {
AthleteID = 35, EventID = 1004, Place = Place.Third
},
new Trial {
AthleteID = 35, EventID = 1005, Place = Place.Third
},
new Trial {
AthleteID = 24, EventID = 1006, Place = Place.Third
},
new Trial {
AthleteID = 27, EventID = 1007, Place = Place.Third
},
new Trial {
AthleteID = 33, EventID = 1008, Place = Place.Third
},
new Trial {
AthleteID = 23, EventID = 1009, Place = Place.Third
},
new Trial {
AthleteID = 10, EventID = 1010, Place = Place.Third
},
new Trial {
AthleteID = 11, EventID = 2001, Place = Place.Third
},
new Trial {
AthleteID = 12, EventID = 2002, Place = Place.Third
},
new Trial {
AthleteID = 13, EventID = 2003, Place = Place.Third
},
new Trial {
AthleteID = 14, EventID = 3001, Place = Place.Third
},
new Trial {
AthleteID = 15, EventID = 3002, Place = Place.Third
},
new Trial {
AthleteID = 16, EventID = 3003, Place = Place.Third
},
new Trial {
AthleteID = 16, EventID = 3004, Place = Place.Third
},
new Trial {
AthleteID = 35, EventID = 1001
},
new Trial {
AthleteID = 35, EventID = 1002
},
new Trial {
AthleteID = 35, EventID = 1003
},
new Trial {
AthleteID = 35, EventID = 1004
},
new Trial {
AthleteID = 35, EventID = 1005
},
new Trial {
AthleteID = 24, EventID = 1006
},
new Trial {
AthleteID = 25, EventID = 1007
},
new Trial {
AthleteID = 33, EventID = 1008
},
new Trial {
AthleteID = 25, EventID = 1009
},
new Trial {
AthleteID = 10, EventID = 1010
},
new Trial {
AthleteID = 11, EventID = 2001
},
new Trial {
AthleteID = 12, EventID = 2002
},
new Trial {
AthleteID = 13, EventID = 2003
},
new Trial {
AthleteID = 14, EventID = 3001
},
new Trial {
AthleteID = 15, EventID = 3002
},
new Trial {
AthleteID = 16, EventID = 3003
},
new Trial {
AthleteID = 16, EventID = 3004
}
};
foreach (Trial e in trials)
{
var enrollmentInDataBase = context.Trials.Where(
s =>
s.Athlete.ID == e.AthleteID &&
s.Event.EventID == e.EventID).SingleOrDefault();
if (enrollmentInDataBase == null)
{
context.Trials.Add(e);
}
}
context.SaveChanges();
}
public void tearDown()
{
EA = null;
}
