public SimulationForBatch MapFrom(Simulation batchSimulation)
{
var individual = _individualMapper.MapFrom(batchSimulation.Individual);
var compounds = batchSimulation.Compounds.Select(_compoundMapper.MapFrom).ToList();
var protocols = batchSimulation.ApplicationProtocols.Select(_protocolMapper.MapFrom).ToList();
var protocolForCompound = new Cache <Model.Compound, Protocol>();
foreach (var applicationProtocol in batchSimulation.ApplicationProtocols)
{
var protocol = _protocolMapper.MapFrom(applicationProtocol);
var compound = compounds.FindByName(applicationProtocol.CompoundName);
if (compound != null)
{
protocolForCompound.Add(compound, protocol);
}
}
//if protocol for compound is not empty, that means that name were specified explictely in json file and we should use that
var protocolToUse = protocolForCompound.Any() ? protocolForCompound.ToList() : protocols;
//a requirement is that compounds and protocols have the same length. Fill missing entries with null
while (protocolToUse.Count < compounds.Count)
{
protocolToUse.Add(null);
}
var modelProperties = _modelPropertiesMapper.MapFrom(batchSimulation.Configuration, individual);
var formulation = _formulationMapper.MapFrom(batchSimulation.Formulation);
var simulationConstruction = new SimulationConstruction
{
SimulationSubject = individual,
TemplateCompounds = compounds,
TemplateProtocols = protocols,
TemplateFormulation = formulation,
ModelProperties = modelProperties,
SimulationName = Simulation.Name,
AllowAging = batchSimulation.Configuration.AllowAging,
Interactions = batchSimulation.Interactions
};
var simulation = _simulationConstructor
.CreateSimulation(simulationConstruction)
.DowncastTo <IndividualSimulation>();
var config = batchSimulation.Configuration;
var interval = simulation.OutputSchema.Intervals.First();
//remove old ones
foreach (var otherInterval in simulation.OutputSchema.Intervals.Skip(1).ToList())
{
simulation.OutputSchema.RemoveInterval(otherInterval);
}
interval.StartTime.Value = config.StartTime;
interval.EndTime.Value = config.EndTime;
interval.Resolution.Value = config.Resolution;
simulation.Solver.AbsTol = config.AbsTol;
simulation.Solver.RelTol = config.RelTol;
_logger.AddDebug($"Start Time = {config.StartTime}");
_logger.AddDebug($"End Time = {config.EndTime}");
_logger.AddDebug($"Resolution = {config.Resolution}");
_logger.AddDebug($"AbsTol = {config.AbsTol}");
_logger.AddDebug($"RelTol = {config.RelTol}");
_logger.AddDebug($"UseJacobian = {config.UseJacobian}");
var simForBatch = new SimulationForBatch
{
Simulation = simulation,
Configuration = config
};
simForBatch.ParameterVariationSets.AddRange(batchSimulation.ParameterVariationSets);
return(simForBatch);
}
public void Visit(ApplicationProtocol protocol)
{
_coreObject = _protocolMapper.MapFrom(protocol);
}