public void ValidateConfigurationFor(Simulation simulation)
{
var compounds = simulation.Compounds;
var simulationSubject = simulation.BuildingBlock <ISimulationSubject>();
var protocols = simulation.Protocols;
var formulations = simulation.AllBuildingBlocks <Formulation>();
var modelConfiguration = simulation.ModelConfiguration;
//ForComp model can only be used with small molecules
if (string.Equals(modelConfiguration.ModelName, CoreConstants.Model.FOUR_COMP) && compounds.Any(x => !x.IsSmallMolecule))
{
throw new InvalidSimulationConfigurationException(PKSimConstants.Error.FourCompModelCannotBeUsedWithLargeMolecule);
}
if (simulation.NameIsOneOf(compounds.AllNames()))
{
throw new InvalidSimulationConfigurationException(PKSimConstants.Error.CompoundAndSimulationCannotShareTheSameName);
}
if (simulation.NameIsOneOf(simulationSubject.AllMolecules().AllNames()))
{
throw new InvalidSimulationConfigurationException(PKSimConstants.Error.IndividualMoleculesAnSimulationCannotShareTheSameName);
}
var schemaItems = protocols.SelectMany(x => _schemaItemsMapper.MapFrom(x)).ToList();
var speciesPopulation = simulationSubject.OriginData.Population;
if (!speciesPopulation.IsBodySurfaceAreaDependent && schemaItems.Any(x => x.DoseIsPerBodySurfaceArea()))
{
throw new InvalidSimulationConfigurationException(PKSimConstants.Error.DosePerBodySurfaceAreaProtocolCannotBeUsedWithSpeciesPopulation(speciesPopulation.DisplayName));
}
if (speciesPopulation.IsNamed(CoreConstants.Population.PREGNANT))
{
throw new InvalidSimulationConfigurationException(PKSimConstants.Error.PregnantPopulationCanOnlyBeUsedWithMoBiModel(speciesPopulation.DisplayName));
}
var administeredCompoundWithSuperSaturationEnabled = compounds.Where(x => x.SupersaturationEnabled).Select(x => new
{
Compound = x,
simulation.CompoundPropertiesFor(x).ProtocolProperties
}).Where(x => x.ProtocolProperties.IsAdministered).Select(x => new
{
x.Compound,
x.ProtocolProperties.Protocol,
x.ProtocolProperties.FormulationMappings
});
administeredCompoundWithSuperSaturationEnabled.Each(x => validateSupersaturationUsageFor(x.Compound, x.Protocol, x.FormulationMappings));
formulations.Where(x => x.FormulationType == CoreConstants.Formulation.TABLE).Each(validateTableFormulation);
}
private IReadOnlyList <ISchemaItem> schemaItemsFrom(Simulation simulation, Compound compound)
{
var protocol = simulation.CompoundPropertiesFor(compound).ProtocolProperties.Protocol;
if (protocol == null)
{
return(new List <ISchemaItem>());
}
return(_protocolToSchemaItemsMapper.MapFrom(protocol));
}
protected override void Context()
{
_simulation = new IndividualSimulation
{
Properties = new SimulationProperties(),
SimulationSettings = new SimulationSettings(),
ModelConfiguration = new ModelConfiguration()
};
_individual = new Individual().WithName("MyIndividual");
_speciesPopulation = new SpeciesPopulation();
_individual.OriginData = new OriginData {
SpeciesPopulation = _speciesPopulation
};
_compound = A.Fake <Compound>().WithName("MyCompound");
_protocol = A.Fake <SimpleProtocol>().WithName("MyProtocol");
_formulation = A.Fake <Formulation>().WithName("Formulation");
_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
});
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Formulation", PKSimBuildingBlockType.Formulation)
{
BuildingBlock = _formulation
});
_protocolToProtocolSchemaItemMapper = A.Fake <IProtocolToSchemaItemsMapper>();
sut = new SimulationConfigurationValidator(_protocolToProtocolSchemaItemMapper);
_speciesPopulation.IsHeightDependent = false;
_schemaItem = A.Fake <SchemaItem>();
_doseUnit = A.Fake <Unit>();
_schemaItem.Dose.DisplayUnit = _doseUnit;
_protocolProperties = new ProtocolProperties();
_formulationMapping = new FormulationMapping {
FormulationKey = "F1", Formulation = _formulation
};
_simulation.Properties.AddCompoundProperties(new CompoundProperties
{
Compound = _compound,
ProtocolProperties = _protocolProperties
});
A.CallTo(() => _protocolToProtocolSchemaItemMapper.MapFrom(_protocol)).Returns(new [] { _schemaItem });
}
private void addProtocol(IEventGroupBuilder applicationSet, CompoundProperties compoundProperties)
{
var protocol = compoundProperties.ProtocolProperties.Protocol;
if (protocol == null)
{
return;
}
var protocolEventGroup = _objectBaseFactory.Create <IEventGroupBuilder>()
.WithName(protocol.Name)
.WithParentContainer(applicationSet);
_schemaItemsMapper.MapFrom(protocol).Each((schemaItem, index) =>
{
//+1 to start at 1 for the nomenclature
string applicationName = $"{CoreConstants.APPLICATION_NAME_TEMPLATE}{index + 1}";
addApplication(protocolEventGroup, schemaItem, applicationName, compoundProperties, protocol);
});
_parameterIdUpdater.UpdateBuildingBlockId(protocolEventGroup, protocol);
}
public void ValidateConfigurationFor(Simulation simulation)
{
var compounds = simulation.Compounds;
var simulationSubject = simulation.BuildingBlock <ISimulationSubject>();
var protocols = simulation.Protocols;
var modelConfiguration = simulation.ModelConfiguration;
//ForComp model can only be used with small molecules
if (string.Equals(modelConfiguration.ModelName, CoreConstants.Model.FourComp) && compounds.Any(x => !x.IsSmallMolecule))
{
throw new InvalidSimulationConfigurationException(PKSimConstants.Error.FourCompModelCannotBeUsedWithLargeMolecule);
}
if (simulation.NameIsOneOf(compounds.AllNames()))
{
throw new InvalidSimulationConfigurationException(PKSimConstants.Error.CompoundAndSimulationCannotShareTheSameName);
}
if (simulation.NameIsOneOf(simulationSubject.AllMolecules().AllNames()))
{
throw new InvalidSimulationConfigurationException(PKSimConstants.Error.IndividualMoleculesAnSimulationCannotShareTheSameName);
}
var schemaItems = protocols.SelectMany(x => _schemaItemsMapper.MapFrom(x)).ToList();
var speciesPopulation = simulationSubject.OriginData.SpeciesPopulation;
if (!speciesPopulation.IsBodySurfaceAreaDependent && schemaItems.Any(x => x.DoseIsPerBodySurfaceArea()))
{
throw new InvalidSimulationConfigurationException(PKSimConstants.Error.DosePerBodySurfaceAreaProtocolCannotBeUsedWithSpeciesPopulation(speciesPopulation.DisplayName));
}
if (speciesPopulation.IsNamed(CoreConstants.Population.Pregnant))
{
throw new InvalidSimulationConfigurationException(PKSimConstants.Error.PregnantPopulationCanOnlyBeUsedWithMoBiModel(speciesPopulation.DisplayName));
}
}
protected override void Context()
{
_vssCalculator = A.Fake <IVSSCalculator>();
_parameterFactory = A.Fake <IParameterFactory>();
_protocolMapper = A.Fake <IProtocolToSchemaItemsMapper>();
_protocolFactory = A.Fake <IProtocolFactory>();
_globalPKAnalysisRunner = A.Fake <IGlobalPKAnalysisRunner>();
_pkCalculationOptionsFactory = A.Fake <IPKCalculationOptionsFactory>();
_pkAnalysisTask = A.Fake <IPKAnalysesTask>();
_interactionTask = A.Fake <IInteractionTask>();
_cloner = A.Fake <ICloner>();
sut = new GlobalPKAnalysisTask(_parameterFactory, _protocolMapper, _protocolFactory, _globalPKAnalysisRunner,
_pkAnalysisTask, _pkCalculationOptionsFactory, _vssCalculator, _interactionTask, _cloner);
var baseGrid = new BaseGrid("time", A.Fake <IDimension>());
_peripheralVenousBloodPlasma = CalculationColumnFor(baseGrid, CoreConstants.Organ.PeripheralVenousBlood, CoreConstants.Observer.PLASMA_PERIPHERAL_VENOUS_BLOOD, CoreConstants.Observer.PLASMA_PERIPHERAL_VENOUS_BLOOD, _compoundName);
_venousBloodPlasma = CalculationColumnFor(baseGrid, CoreConstants.Organ.VenousBlood, CoreConstants.Compartment.Plasma, CoreConstants.Observer.CONCENTRATION_IN_CONTAINER, _compoundName);
_individual = A.Fake <Individual>();
_species = new Species();
A.CallTo(() => _individual.Species).Returns(_species);
_compound = new Compound().WithName(_compoundName);
_compoundProperties = new CompoundProperties {
Compound = _compound
};
_simulationSchemaItems = new List <SchemaItem>();
_protocol = new SimpleProtocol();
_compoundProperties.ProtocolProperties.Protocol = _protocol;
A.CallTo(() => _protocolMapper.MapFrom(_protocol)).Returns(_simulationSchemaItems);
_simulation = new IndividualSimulation {
Properties = new SimulationProperties()
};
_simulation.Properties.AddCompoundProperties(_compoundProperties);
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("CompId", PKSimBuildingBlockType.Compound)
{
BuildingBlock = _compound
});
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("IndividualId", PKSimBuildingBlockType.Individual)
{
BuildingBlock = _individual
});
_simulation.DataRepository = new DataRepository {
_venousBloodPlasma, _peripheralVenousBloodPlasma
};
_venousBloodPK = new PKValues();
_venousBloodPK.AddValue(Constants.PKParameters.Vss, 10);
_venousBloodPK.AddValue(Constants.PKParameters.Vd, 11);
_venousBloodPK.AddValue(Constants.PKParameters.CL, 12);
_venousBloodPK.AddValue(Constants.PKParameters.AUC_inf, 13);
_venousBloodPK.AddValue(Constants.PKParameters.AUC_inf_tD1_norm, 14);
_peripheralVenousBloodPK = new PKValues();
_peripheralVenousBloodPK.AddValue(Constants.PKParameters.Vss, 21);
_peripheralVenousBloodPK.AddValue(Constants.PKParameters.Vd, 22);
_peripheralVenousBloodPK.AddValue(Constants.PKParameters.CL, 23);
_peripheralVenousBloodPK.AddValue(Constants.PKParameters.AUC_inf, 24);
_peripheralVenousBloodPK.AddValue(Constants.PKParameters.AUC_inf_tD1_norm, 25);
_peripheralVenousBloodPK.AddValue(Constants.PKParameters.C_max, 26);
_peripheralVenousBloodPK.AddValue(Constants.PKParameters.C_max_tDLast_tDEnd, 27);
A.CallTo(() => _pkAnalysisTask.CalculatePK(_venousBloodPlasma, A <PKCalculationOptions> ._)).Returns(_venousBloodPK);
A.CallTo(() => _pkAnalysisTask.CalculatePK(_peripheralVenousBloodPlasma, A <PKCalculationOptions> ._)).Returns(_peripheralVenousBloodPK);
A.CallTo(() => _parameterFactory.CreateFor(A <string> ._, A <double> ._, A <string> ._, PKSimBuildingBlockType.Simulation))
.ReturnsLazily(s => new PKSimParameter().WithName((string)s.Arguments[0])
.WithDimension(A.Fake <IDimension>())
.WithFormula(new ConstantFormula((double)s.Arguments[1])));
}
private IReadOnlyList <SchemaItemDTO> schemaItemsDTOFrom(Protocol protocol)
{
return(_schemaItemsMapper.MapFrom(protocol).MapAllUsing(_schemaItemDTOMapper));
}
