protected override void Context()
{
base.Context();
_eventGroupBuildingBlock = new EventGroupBuildingBlock();
_eventGroup = new EventGroupBuilder().WithName("EG");
_eventGroupBuildingBlock.Add(_eventGroup);
var parameter = new Parameter().WithName("P1").WithParentContainer(_eventGroup);
}
protected override void Context()
{
base.Context();
var eg1 = new EventGroupBuilder().WithName("Events");
var e1 = new EventBuilder().WithName("Start").WithParentContainer(eg1);
var eg2 = new EventGroupBuilder().WithName("Events");
var e2 = new EventBuilder().WithName("Stop").WithParentContainer(eg2);
_object1 = eg1;
_object2 = eg2;
}
protected override void Context()
{
base.Context();
var eg1 = new EventGroupBuilder().WithName("Events");
var e1 = new EventBuilder().WithName("Start").WithParentContainer(eg1);
eg1.SourceCriteria = Create.Criteria(x => x.With("A").And.Not("B"));
var eg2 = new EventGroupBuilder().WithName("Events");
var e2 = new EventBuilder().WithName("Start").WithParentContainer(eg2);
eg2.SourceCriteria = Create.Criteria(x => x.With("B").And.Not("A"));
_object1 = eg1;
_object2 = eg2;
}
/// <summary>
/// Creates a EventGroupBuildingBlock and a EventGroupBuilder.
/// </summary>
internal void CreateEGBandEGBB()
{
EventGroupBuilder = new EventGroupBuilder()
.WithName(SBMLConstants.SBML_EVENTS)
.WithId(SBMLConstants.SBML_EVENTS);
var eventsContainer = GetEventsTopContainer();
if (eventsContainer != null)
{
var matchTag = new MatchTagCondition(eventsContainer.Name);
EventGroupBuilder.SourceCriteria.Add(matchTag);
}
EventGroupBuildingBlock = new EventGroupBuildingBlock()
.WithName(SBMLConstants.SBML_EVENT_BB)
.WithId(SBMLConstants.SBML_EVENT_BB);
EventGroupBuildingBlock.Add(EventGroupBuilder);
}
protected override void Context()
{
base.Context();
_project = new MoBiProject();
var molecule = new MoleculeBuilder().WithName(_moleculeName);
var moleculeParameter = new Parameter().WithName(_moleculeParameterName);
molecule.Add(moleculeParameter);
var molecules = new MoleculeBuildingBlock()
{
molecule
};
_project.AddBuildingBlock(molecules);
var parameter = new Parameter().WithName(_parameterName);
var root = new Container().WithName(_topContainerName);
root.Add(parameter);
var spatialStructure = new MoBiSpatialStructure().WithTopContainer(root);
spatialStructure.GlobalMoleculeDependentProperties = new Container().WithName(Constants.MOLECULE_PROPERTIES);
spatialStructure.NeighborhoodsContainer = new Container().WithName(Constants.NEIGHBORHOODS);
_project.AddBuildingBlock(spatialStructure);
var reactionBuilder = new ReactionBuilder().WithName(_reactionName);
var reactions = new MoBiReactionBuildingBlock()
{
reactionBuilder
};
_project.AddBuildingBlock(reactions);
_project.AddSimulation(new MoBiSimulation().WithName(_simulationName));
var eventGroupBuilder = new EventGroupBuilder().WithName(_eventGroupName);
var eventGroupBuildingBlock = new EventGroupBuildingBlock();
eventGroupBuildingBlock.Add(eventGroupBuilder);
_project.AddBuildingBlock(eventGroupBuildingBlock);
A.CallTo(() => _context.CurrentProject).Returns(_project);
}
protected override void Context()
{
base.Context();
var observerBuildingBlock1 = new EventGroupBuildingBlock().WithName("Tada");
IEventGroupBuilder observerBuilderA = new ApplicationBuilder().WithName("EGA");
var observerBuilderB = new ApplicationBuilder().WithName("EGB");
observerBuildingBlock1.Add(observerBuilderA);
observerBuildingBlock1.Add(observerBuilderB);
var observerBuildingBlock2 = new EventGroupBuildingBlock().WithName("Tada");
observerBuilderA = new EventGroupBuilder().WithName("EGA");
observerBuilderB = new ApplicationBuilder().WithName("EGB");
observerBuildingBlock2.Add(observerBuilderA);
observerBuildingBlock2.Add(observerBuilderB);
_object1 = observerBuildingBlock1;
_object2 = observerBuildingBlock2;
}
protected override void Context()
{
base.Context();
_eventGroupBuildingBlock = new EventGroupBuildingBlock();
var eventGroup = new EventGroupBuilder().WithName("EG");
_eventGroupBuildingBlock.Add(eventGroup);
var ehcStartEvent = new EventBuilder().WithName(Converter321To331.EHCStartEvent);
eventGroup.Add(ehcStartEvent);
var eabOldStart = new EventAssignmentBuilder().WithName("EAB1").WithFormula(new ExplicitFormula("ln(2) / EHC_Halftime * M * EHC_EjectionFraction"));
eabOldStart.UseAsValue = false;
eabOldStart.ObjectPath = new ObjectPath(new[] { "Organism", "Gallbladder", "Gallbladder emptying rate" });
ehcStartEvent.AddAssignment(eabOldStart);
var assignmentBuilder = new EventAssignmentBuilder().WithName("EAB2").WithFormula(new ExplicitFormula("DontChange"));
assignmentBuilder.ObjectPath = new ObjectPath(new[] { "PATH" });
ehcStartEvent.AddAssignment(assignmentBuilder);
var ehcStopEvent = new EventBuilder().WithName(Converter321To331.EHCStopEvent);
var eabOldStop = new EventAssignmentBuilder().WithName("EAB1").WithFormula(new ConstantFormula(0));
eabOldStop.UseAsValue = false;
eabOldStop.ObjectPath = new ObjectPath(new[] { "Organism", "Gallbladder", "Gallbladder emptying rate" });
ehcStopEvent.AddAssignment(eabOldStop);
assignmentBuilder = new EventAssignmentBuilder().WithName("EAB2").WithFormula(new ExplicitFormula("DontChange"));
assignmentBuilder.ObjectPath = new ObjectPath(new[] { "PATH" });
ehcStopEvent.AddAssignment(assignmentBuilder);
eventGroup.Add(ehcStopEvent);
var protocolSchemaItem = new Container().WithName("ProtocolSchemaItem").WithParentContainer(eventGroup);
_drugMassParameter = new Parameter().WithName("DrugMass").WithParentContainer(protocolSchemaItem).WithValue(1);
applications = new EventGroupBuilder().WithName("Applications");
applications.Add(new Parameter().WithName("TotalDrugMass"));
_eventGroupBuildingBlock.Add(applications);
}
public void TestSerialization()
{
EventGroupBuilder x1 = CreateObject <EventGroupBuilder>().WithName("Evan.Builder");
x1.EventGroupType = "IV Bolus";
IFormula f1 = CreateObject <ConstantFormula>().WithValue(2.3);
IFormula f2 = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(3.4);
IParameter p1 = CreateObject <Parameter>().WithName("Patricia").WithFormula(f1).WithValue(3.1);
IParameter p2 = CreateObject <Parameter>().WithName("Pascal").WithFormula(f1).WithValue(3.2);
x1.Add(p1);
x1.Add(p2);
EventBuilder eb1 = CreateObject <EventBuilder>().WithName("Eve.Builder").WithDimension(DimensionLength).WithFormula(f1);
EventBuilder eb2 = CreateObject <EventBuilder>().WithName("Eva.Builder").WithDimension(DimensionLength).WithFormula(f2);
eb2.OneTime = true;
x1.Add(eb1);
x1.Add(eb2);
ApplicationBuilder a1 = CreateObject <ApplicationBuilder>().WithName("App.Builder");
x1.Add(a1);
var applicationMoleculeBuilder = CreateObject <ApplicationMoleculeBuilder>().WithName("AppMolecule");
applicationMoleculeBuilder.Formula = f2;
applicationMoleculeBuilder.RelativeContainerPath = new ObjectPath(new[] { "A", "B" });
a1.AddMolecule(applicationMoleculeBuilder);
a1.AddTransport(CreateObject <TransportBuilder>().WithName("PassiveTranport").WithFormula(f1));
IEventGroupBuilder x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualEventGroupBuilder(x1, x2);
}
protected override void Context()
{
base.Context();
var eg1 = new EventGroupBuilder().WithName("Events");
var app1 = new ApplicationBuilder().WithName("App").WithParentContainer(eg1);
app1.MoleculeName = "Drug";
var c1 = new Container().WithName("ProtocolSchemaItem").WithParentContainer(app1);
_e1 = new EventBuilder().WithName("Event").WithParentContainer(app1);
_eventAssignmentBuilder1 = new EventAssignmentBuilder();
_eventAssignmentBuilder1.ObjectPath = new ObjectPath("Sim|A|B|C");
_eventAssignmentBuilder1.Name = "EAB";
_eventAssignmentBuilder1.UseAsValue = true;
_eventAssignmentBuilder1.Formula = new ExplicitFormula("a+b");
_e1.AddAssignment(_eventAssignmentBuilder1);
_explicitFormula1 = new ExplicitFormula("1+2");
_p1 = new Parameter().WithName("P").WithFormula(_explicitFormula1).WithParentContainer(c1);
var eg2 = new EventGroupBuilder().WithName("Events");
var app2 = new ApplicationBuilder().WithName("App").WithParentContainer(eg2);
app2.MoleculeName = "Drug";
var c2 = new Container().WithName("ProtocolSchemaItem").WithParentContainer(app2);
var e2 = new EventBuilder().WithName("Event").WithParentContainer(app2);
var eventAssignmentBuilder2 = new EventAssignmentBuilder();
eventAssignmentBuilder2.ObjectPath = new ObjectPath("Sim|A|B|C");
eventAssignmentBuilder2.Name = "EAB";
eventAssignmentBuilder2.UseAsValue = false;
eventAssignmentBuilder2.Formula = new ExplicitFormula("a+b");
e2.AddAssignment(eventAssignmentBuilder2);
var p2 = new Parameter().WithName("P").WithFormula(new ExplicitFormula("2+1")).WithParentContainer(c2);
_object1 = eg1;
_object2 = eg2;
}
