private void updatePersistableFor(IndividualSimulation simulation, bool exportAll)
{
if (exportAll)
{
_simulationPersistableUpdater.ResetPersistable(simulation);
}
else
{
_simulationPersistableUpdater.UpdatePersistableFromSettings(simulation);
}
}
private async Task runSimulation <TSimulation>(TSimulation simulation, Action <TSimulation> updatePersistableFromSettings) where TSimulation : Simulation
{
var simulationEngine = _simulationEngineFactory.Create <TSimulation>();
_simulationEngine = simulationEngine;
if (_simulationRunOptions.RunForAllOutputs)
{
_simulationPersistableUpdater.ResetPersistable(simulation);
}
else
{
updatePersistableFromSettings(simulation);
}
await simulationEngine.RunAsync(simulation, _simulationRunOptions);
simulation.HasChanged = true;
}
private void updateSimulationAfterModelCreation(Simulation simulation)
{
//last step. Once the model has been created, it is necessary to set the id of the simulation
//in all parameter defined in the model
_parameterIdUpdater.UpdateSimulationId(simulation);
//local molecule parameters parameter id need to be updated as well
var allParameters = _containerTask.CacheAllChildren <IParameter>(simulation.Model.Root);
var individual = simulation.Individual;
individual.AllMolecules().Each(m =>
{
var allMoleculeParameters = individual.AllMoleculeParametersFor(m);
allMoleculeParameters.Each(p =>
{
var simulationParameter = allParameters[_entityPathResolver.PathFor(p)];
if (simulationParameter != null)
{
updateFromIndividualParameter(simulationParameter, p, individual);
}
});
});
//we need to update the observer types according to their location (container observer are always of type drug, amount observer are depending on parent)
var allObservers = simulation.All <IObserver>();
foreach (var observer in allObservers)
{
var quantity = observer.ParentContainer as IQuantity;
if (quantity != null)
{
observer.QuantityType = QuantityType.Observer | quantity.QuantityType;
}
else
{
observer.QuantityType = QuantityType.Observer | QuantityType.Drug;
}
}
_simulationPersistableUpdater.ResetPersistable(simulation);
}
private void updateSimulationAfterModelCreation(Simulation simulation)
{
//last step. Once the model has been created, it is necessary to set the id of the simulation
//in all paramater defined in the model
_parameterIdUpdater.UpdateSimulationId(simulation);
var allMoleculeAmounts = simulation.All <IMoleculeAmount>().ToList();
//local molecule parameters parameter id need to be updated as well
var allIndividualMoleculeAmounts = allMoleculeAmounts.Where(m => m.IsIndividualMolecule());
var individual = simulation.Individual;
var allOrganismContainers = _expressionContainersRetriever.AllOrganismContainers(individual).ToList();
hideAllUndefinedParameterForMolecules(simulation);
foreach (var moleculeAmountGroup in allIndividualMoleculeAmounts.GroupBy(x => x.Name))
{
var molecule = individual.MoleculeByName <IndividualMolecule>(moleculeAmountGroup.Key);
var moleculeAmountPath = new PathCache <IMoleculeAmount>(_entityPathResolver).For(moleculeAmountGroup);
updateAllParametersFor(simulation, individual, allOrganismContainers, molecule, moleculeAmountPath);
}
//we need to update the observer types according to their location (container observer are always of type drug, amount observer are depending on parent)
var allObservers = simulation.All <IObserver>();
foreach (var observer in allObservers)
{
var quantity = observer.ParentContainer as IQuantity;
if (quantity != null)
{
observer.QuantityType = QuantityType.Observer | quantity.QuantityType;
}
else
{
observer.QuantityType = QuantityType.Observer | QuantityType.Drug;
}
}
_simulationPersistableUpdater.ResetPersistable(simulation);
}