public Simulation CreateSimulation(SimulationConstruction simulationConstruction, Action <Simulation> preModelCreationAction = null)
{
var simulation = _simulationConstructor.CreateSimulation(simulationConstruction, preModelCreationAction);
AddSimulationClassificationFor(simulation);
return(simulation);
}
private async Task <IBuildConfiguration> configurationFrom(SimulationConstruction simulationConstruction)
{
var simulation = await _snapshotObjectCreator.SimulationFor(simulationConstruction);
return(_buildConfigurationTask.CreateFor(simulation, shouldValidate: false, createAgingDataInSimulation: false));
}
private async Task exportToFolder(string exportFolder)
{
var project = new Project();
var individual = await _snapshotObjectCreator.DefaultIndividual();
project.Individuals = new[] { individual };
var compound = await _snapshotObjectCreator.StandardCompound(lipophilicity : 3, fractionUnbound : 0.1, molWeight : 400, name : "Standard Molecule");
compound.Name = "Standard Molecule";
project.Compounds = new[] { compound };
var intrevanousBolusMgPerKg = await _snapshotObjectCreator.SimpleProtocol(dose : 1, doseUnit : "mg/kg", applicationType : ApplicationTypes.IntravenousBolus);
var intrevanousBolusMg = await _snapshotObjectCreator.SimpleProtocol(dose : 1, doseUnit : "mg", applicationType : ApplicationTypes.IntravenousBolus);
project.Protocols = new[] { intrevanousBolusMgPerKg, intrevanousBolusMg };
var snapshotConfiguration = new SimulationConstruction
{
Individual = individual,
Compounds = new[] { compound },
Protocols = new [] { intrevanousBolusMgPerKg },
ModelName = CoreConstants.Model.FourComp,
};
var fourCompIvBolusMgPerKg = await configurationFrom(snapshotConfiguration);
snapshotConfiguration.ModelName = CoreConstants.Model.TwoPores;
var twoPore = await configurationFrom(snapshotConfiguration);
snapshotConfiguration.Protocols = new[] { intrevanousBolusMg };
snapshotConfiguration.ModelName = CoreConstants.Model.FourComp;
var fourCompIvBolusMg = await configurationFrom(snapshotConfiguration);
twoPore.SpatialStructure.Name = "Human 2 Pores";
twoPore.PassiveTransports.Name = "2 Pores Passive Transports";
fourCompIvBolusMgPerKg.SpatialStructure.Name = "Human Standard";
fourCompIvBolusMgPerKg.PassiveTransports.Name = "Standard Passive Transports";
fourCompIvBolusMgPerKg.EventGroups.Name = "IV Bolus";
fourCompIvBolusMgPerKg.Molecules.Name = "Standard Molecule";
fourCompIvBolusMgPerKg.Observers.Name = "Standard Observer";
fourCompIvBolusMg.EventGroups.Name = "IV Bolus (mg)";
var defaultCompound = fourCompIvBolusMgPerKg.Molecules.First();
defaultCompound.Name = string.Empty;
defaultCompound.Parameter(CoreConstants.Parameters.LIPOPHILICITY).Value = double.NaN;
defaultCompound.Parameter(CoreConstants.Parameters.MOLECULAR_WEIGHT).Value = double.NaN;
defaultCompound.Parameter(CoreConstants.Parameters.FRACTION_UNBOUND_PLASMA_REFERENCE_VALUE).Value = double.NaN;
defaultCompound.Parameter(CoreConstants.Parameters.SOLUBILITY_AT_REFERENCE_PH).Value = double.NaN;
_moBiExportTask.UpdateObserverForAllFlag(fourCompIvBolusMgPerKg.Observers);
var buildingBlocks = new IBuildingBlock[]
{
twoPore.SpatialStructure,
twoPore.PassiveTransports,
fourCompIvBolusMgPerKg.SpatialStructure,
fourCompIvBolusMgPerKg.PassiveTransports,
fourCompIvBolusMgPerKg.EventGroups,
fourCompIvBolusMgPerKg.Molecules,
fourCompIvBolusMgPerKg.Observers,
fourCompIvBolusMg.EventGroups
};
buildingBlocks.Each(bb => saveToPKML(bb, exportFolder));
}
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);
}