protected override void Context()
{
_spatialStructureFactory = A.Fake <IPKSimSpatialStructureFactory>();
_modelObserverQuery = A.Fake <IModelObserverQuery>();
_modelPassiveTransportQuery = A.Fake <IModelPassiveTransportQuery>();
_parameterStartValueCreator = A.Fake <IPKSimParameterStartValuesCreator>();
_moleculesAndReactionsCreator = A.Fake <IMoleculesAndReactionsCreator>();
_eventBuildingBlockCreator = A.Fake <IEventBuildingBlockCreator>();
_moleculeStartValueCreator = A.Fake <IPKSimMoleculeStartValuesCreator>();
_moleculeCalculationRetriever = A.Fake <IMoleculeCalculationRetriever>();
_distributedTableConverter = A.Fake <IDistributedParameterToTableParameterConverter>();
_parameterDefaultStateUpdater = A.Fake <IParameterDefaultStateUpdater>();
_cm1 = new CoreCalculationMethod();
_cm2 = new CoreCalculationMethod();
_simulation = new IndividualSimulation {
Properties = new SimulationProperties()
};
_simulation.SimulationSettings = new SimulationSettings();
_simulation.ModelConfiguration = new ModelConfiguration();
_individual = new Individual().WithName("MyIndividuyal");
_compound = A.Fake <Compound>().WithName("MyCompound");
_protocol = new SimpleProtocol().WithName("MyProtocol");
_spatialStructure = A.Fake <ISpatialStructure>();
_passiveTransportBuilingBlock = A.Fake <IPassiveTransportBuildingBlock>();
_observerBuildingBlock = A.Fake <IObserverBuildingBlock>();
_eventBuildingBlock = A.Fake <IEventGroupBuildingBlock>();
_parameterValuesBuildingBlock = A.Fake <IParameterStartValuesBuildingBlock>();
_moleculeStartValueBuildingBlock = A.Fake <IMoleculeStartValuesBuildingBlock>();
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Individual", PKSimBuildingBlockType.Individual)
{
BuildingBlock = _individual
});
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Compound", PKSimBuildingBlockType.Compound)
{
BuildingBlock = _compound
});
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Protocol", PKSimBuildingBlockType.Protocol)
{
BuildingBlock = _protocol
});
A.CallTo(() => _moleculeCalculationRetriever.AllMoleculeCalculationMethodsUsedBy(_simulation)).Returns(new[] { _cm1, _cm2 });
A.CallTo(() => _spatialStructureFactory.CreateFor(_individual, _simulation)).Returns(_spatialStructure);
A.CallTo(() => _modelPassiveTransportQuery.AllPassiveTransportsFor(_simulation)).Returns(_passiveTransportBuilingBlock);
A.CallTo(() => _modelObserverQuery.AllObserversFor(A <IMoleculeBuildingBlock> .Ignored, _simulation)).Returns(_observerBuildingBlock);
A.CallTo(() => _eventBuildingBlockCreator.CreateFor(_simulation)).Returns(_eventBuildingBlock);
A.CallTo(() => _parameterStartValueCreator.CreateFor(A <IBuildConfiguration> .Ignored, A <Simulation> .Ignored)).Returns(_parameterValuesBuildingBlock);
A.CallTo(() => _moleculeStartValueCreator.CreateFor(A <IBuildConfiguration> .Ignored, A <Simulation> .Ignored)).Returns(_moleculeStartValueBuildingBlock);
sut = new BuildConfigurationTask(_spatialStructureFactory, _modelObserverQuery, _modelPassiveTransportQuery, _parameterStartValueCreator,
_moleculesAndReactionsCreator, _eventBuildingBlockCreator, _moleculeStartValueCreator, _moleculeCalculationRetriever,
_distributedTableConverter, _parameterDefaultStateUpdater);
}
public IBuildConfiguration CreateFor(Simulation simulation, bool shouldValidate, bool createAgingDataInSimulation)
{
var buildConfiguration = new BuildConfiguration {
ShouldValidate = shouldValidate
};
var individual = simulation.Individual;
//STEP1: Create spatial structure
buildConfiguration.SpatialStructure = _spatialStructureFactory.CreateFor(individual, simulation);
_parameterDefaultStateUpdater.UpdateDefaultFor(buildConfiguration.SpatialStructure);
//STEP2: add used calculation method to the build configuration
_moleculeCalculationRetriever.AllMoleculeCalculationMethodsUsedBy(simulation).Each(buildConfiguration.AddCalculationMethod);
//STEP3: Add Passive Transports
buildConfiguration.PassiveTransports = _modelPassiveTransportQuery.AllPassiveTransportsFor(simulation)
.WithName(simulation.Name);
//STEP4 : Molecules, and Molecule Start and reactions are generated in one go from the molecule and reaction creator
_moleculesAndReactionsCreator.CreateFor(buildConfiguration, simulation);
//STEP5 Add Application, Formulation and events
buildConfiguration.EventGroups = _eventBuildingBlockCreator.CreateFor(simulation);
_parameterDefaultStateUpdater.UpdateDefaultFor(buildConfiguration.EventGroups);
//STEP6: Add Observers
buildConfiguration.Observers = _modelObserverQuery.AllObserversFor(buildConfiguration.Molecules, simulation);
//STEP7 once all building blocks have been created, we need to create the default parameter and molecule values values
buildConfiguration.MoleculeStartValues = _moleculeStartValuesCreator.CreateFor(buildConfiguration, simulation);
buildConfiguration.ParameterStartValues = _parameterStartValuesCreator.CreateFor(buildConfiguration, simulation);
//STEP8 update simulation settings
buildConfiguration.SimulationSettings = simulation.SimulationSettings.WithName(simulation.Name);
//STEP9 Convert all parameters to table if required
_distributedParameterToTableParameterConverter.UpdateBuildConfigurationForAging(buildConfiguration, simulation, createAgingDataInSimulation);
return(buildConfiguration);
}
