protected override void Because()
{
var model = new Model(3, 1);
model.setName("TestModel");
model.setNotes("TestNotes");
model.setMetaId("TestMetaId");
sut.CreateEventsTopContainer();
sut.CreateTopContainer(model);
var compartment = new Compartment(3, 1);
compartment.setName("Compartment");
compartment.setId("c1");
compartment.setSpatialDimensions(1);
compartment.setSize(5);
var compartment2 = new Compartment(3, 1);
compartment2.setName("Compartment");
compartment2.setId("c2");
compartment2.setSpatialDimensions(2);
compartment2.setSize(5);
var compartment3 = new Compartment(3, 1);
compartment3.setName("Compartment");
compartment3.setId("c3");
compartment3.setSpatialDimensions(3);
compartment3.setSize(5);
_container = sut.CreateContainerFromCompartment(compartment);
_container2 = sut.CreateContainerFromCompartment(compartment2);
_container3 = sut.CreateContainerFromCompartment(compartment3);
sut.CreateSpatialStructureFromModel(sut._topContainer, model);
}
public override void GlobalContext()
{
base.GlobalContext();
_fourCompSim = DomainFactoryForSpecs.CreateDefaultSimulationForModel(CoreConstants.Model.FOUR_COMP);
_fourComp = _fourCompSim.Model.Root.Container(Constants.ORGANISM);
_twoPoresSim = DomainFactoryForSpecs.CreateDefaultSimulationForModel(CoreConstants.Model.TWO_PORES);
_twoPores = _twoPoresSim.Model.Root.Container(Constants.ORGANISM);
_organisms = new List <IContainer> {
_fourComp, _twoPores
};
}
public override void GlobalContext()
{
base.GlobalContext();
_buildConfiguration = DomainFactoryForSpecs.CreateDefaultConfiguration();
var spatialStructure = _buildConfiguration.SpatialStructure;
_organism = spatialStructure.TopContainers.ElementAt(0);
var volumeParameter = _organism.EntityAt <IParameter>(Constants.Parameters.VOLUME);
volumeParameter.Persistable = true;
_simulation = DomainFactoryForSpecs.CreateSimulationFor(_buildConfiguration);
var simulationRunner = IoC.Resolve <ISimulationRunner>();
simulationRunner.RunSimulation(_simulation);
}
protected override void Context()
{
_spatialStructureDiagramManager = A.Fake <ISpatialStructureDiagramManager>();
_spatialStructure = new MoBiSpatialStructure {
DiagramManager = _spatialStructureDiagramManager
}.WithName("SpSt");
_spatialStructure.NeighborhoodsContainer = new Container().WithName(Constants.NEIGHBORHOODS);
_parent = new Container().WithName("Top").WithMode(ContainerMode.Logical).WithId(_parentId);
_containerToRemove = new Container().WithName("A").WithMode(ContainerMode.Physical).WithParentContainer(_parent);
_otherContainer = new Container().WithName("B").WithMode(ContainerMode.Physical).WithParentContainer(_parent);
_spatialStructure.AddTopContainer(_parent);
_neighborhood = new NeighborhoodBuilder().WithFirstNeighbor(_containerToRemove).WithSecondNeighbor(_otherContainer).WithName("A2B");
_spatialStructure.AddNeighborhood(_neighborhood);
_context = A.Fake <IMoBiContext>();
sut = new RemoveContainerFromSpatialStructureCommand(_parent, _containerToRemove, _spatialStructure);
}
private bool isPureContainer(IContainer container)
{
return(!container.IsAnImplementationOf <IEventGroupBuilder>() &&
!container.IsAnImplementationOf <IEventBuilder>() &&
!container.IsAnImplementationOf <ITransportBuilder>());
}
private IEnumerable <string> reactionNamesIn(IContainer container)
{
return((from molecule in container.GetAllChildren <IReaction>()
select molecule.Name).ToList());
}
private IEnumerable <string> moleculeNamesIn(IContainer container)
{
return((from molecule in container.GetAllChildren <IMoleculeAmount>()
select molecule.Name).ToList());
}
private IParameter startValueFor(IContainer molecule)
{
return(molecule.EntityAt <IParameter>(Constants.Parameters.START_VALUE));
}
public override void GlobalContext()
{
base.GlobalContext();
_simulation = IoC.Resolve <ConcentrationBaseModelHelperForSpecs>().CreateSimulation();
_organism = _simulation.Model.Root.GetSingleChildByName <IContainer>(ConstantsForSpecs.Organism);
}
public void Run(IContainer root)
{
root.AcceptVisitor(this);
}
private IParameter organParameterFor(IContainer root, string organName, string parameterName)
{
return root.Container(Constants.ORGANISM)
.Container(organName).Parameter(parameterName);
}
private double LITTFor(IContainer individual)
{
return organParameterFor(individual, CoreConstants.Organ.LargeIntestine, ConverterConstants.Parameter.LITT).Value;
}
