protected override void Context()
{
base.Context();
_pkValues = new PKValues();
_pkValues.AddValue("P1", 10f);
_pkValues.AddValue("P2", 10f);
_mode = PKParameterMode.Single;
_drugName = "TOTO";
_pk1 = new PKParameter {
Mode = _mode, Name = "P1", Dimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs()
};
_pk2 = new PKParameter {
Mode = _mode, Name = "P2", Dimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs()
};
_pk3 = new PKParameter {
Mode = PKParameterMode.Multi, Name = "P3"
};
var baseGrid = new BaseGrid("Time", DomainHelperForSpecs.TimeDimensionForSpecs());
_col = new DataColumn("COL", DomainHelperForSpecs.ConcentrationDimensionForSpecs(), baseGrid)
{
DataInfo = { MolWeight = 150 }
};
A.CallTo(() => _pkParameterRepository.All()).Returns(new [] { _pk1, _pk2, _pk3 });
A.CallTo(() => _parameterFactory.CreateFor(A <string> ._, A <double> ._, A <string> ._, PKSimBuildingBlockType.Simulation))
.ReturnsLazily(x => DomainHelperForSpecs.ConstantParameterWithValue(x.GetArgument <double>(1)).WithName(x.GetArgument <string>(0)));
}
protected override void Context()
{
base.Context();
_simulation = A.Fake <ISimulation>();
_runResults = A.Fake <SimulationResults>();
var outputSelections = new OutputSelections();
outputSelections.AddOutput(new QuantitySelection("Liver|Cell|Drug|Concentration", QuantityType.Drug));
A.CallTo(() => _simulation.OutputSelections).Returns(outputSelections);
var pKCalculationOptions = new PKCalculationOptions();
A.CallTo(_pkCalculationOptionsFactory).WithReturnType <PKCalculationOptions>().Returns(pKCalculationOptions);
_p1 = new PKParameter().WithName("AUC");
_p1.Mode = PKParameterMode.Single;
_p2 = new PKParameter().WithName("AUC" + Constants.PKParameters.NormSuffix);
_p2.Mode = PKParameterMode.Single;
A.CallTo(() => _pkParameterRepository.All()).Returns(new[] { _p1, _p2 });
var individualResults = A.Fake <IndividualResults>();
A.CallTo(() => _runResults.AllIndividualResults).Returns(new HashSet <IndividualResults>(new [] { individualResults }));
var pKValues = new PKValues();
pKValues.AddValue(_p1.Name, 10f);
pKValues.AddValue(_p2.Name, 20f);
A.CallTo(_pkValuesCalculator).WithReturnType <PKValues>().Returns(pKValues);
}
protected override void Context()
{
base.Context();
_simulation = A.Fake <ISimulation>();
_runResults = A.Fake <SimulationResults>();
var outputSelections = new OutputSelections();
outputSelections.AddOutput(new QuantitySelection("Liver|Cell|Drug|Concentration", QuantityType.Drug));
A.CallTo(() => _simulation.OutputSelections).Returns(outputSelections);
var pKCalculationOptions = new PKCalculationOptions();
A.CallTo(_pkCalculationOptionsFactory).WithReturnType <PKCalculationOptions>().Returns(pKCalculationOptions);
_p1 = new PKParameter {
Name = "AUC", Mode = PKParameterMode.Single
};
_userDefinedParameter1 = new UserDefinedPKParameter {
Name = "Dynamic1", Mode = PKParameterMode.Single
};
A.CallTo(() => _pkParameterRepository.All()).Returns(new[] { _p1, _userDefinedParameter1 });
var individualResults = A.Fake <IndividualResults>();
A.CallTo(() => _runResults.AllIndividualResults).Returns(new HashSet <IndividualResults>(new[] { individualResults }));
var pKValues = new PKValues();
pKValues.AddValue(_p1.Name, 10f);
pKValues.AddValue(_userDefinedParameter1.Name, 30f);
A.CallTo(_pkValuesCalculator).WithReturnType <PKValues>().Returns(pKValues);
}
public PKAnalysis MapFrom(DataColumn dataColumn, PKValues pkValues, PKParameterMode mode, string moleculeName)
{
var pk = new PKAnalysis().WithName(moleculeName);
_pkParameterRepository.All().Where(parameter => parameter.Mode.Is(mode)).Each(parameter => pk.Add(createPKParameter(parameter, pkValues)));
pk.MolWeight = dataColumn.DataInfo.MolWeight;
return(pk);
}
private PKValues pkValuesFrom(ICache <string, double> pk)
{
var pkValues = new PKValues();
foreach (var pkValue in pk.KeyValues)
{
pkValues.AddValue(pkValue.Key, pkValue.Value.ConvertedTo <float>());
}
return(pkValues);
}
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 IParameter createPKParameter(PKParameter pkParameter, PKValues pkValues)
{
return(createPKParameter(pkParameter.Name, pkValues.ValueOrDefaultFor(pkParameter.Name), pkParameter.Dimension.Name));
}
protected override void Because()
{
_pk = sut.CalculatePK(_multipleDosingColumn, _pkOptions);
}
protected override void Because()
{
_pk = sut.CalculatePK(_emptyColums, _pkOptions);
}
protected override void Because()
{
_pk = sut.CalculatePK(_singleDosing, _pkOptions);
}
protected override void Because()
{
_pk = sut.CalculatePK(_multipleDosingColumn, _pkOptions, _allDynamicPkParameters);
}
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.PERIPHERAL_VENOUS_BLOOD, CoreConstants.Observer.PLASMA_PERIPHERAL_VENOUS_BLOOD, CoreConstants.Observer.PLASMA_PERIPHERAL_VENOUS_BLOOD, _compoundName);
_venousBloodPlasma = CalculationColumnFor(baseGrid, CoreConstants.Organ.VENOUS_BLOOD, 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
};
_protocol = new SimpleProtocol();
_compoundProperties.ProtocolProperties.Protocol = _protocol;
_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
};
_simulation.SimulationSettings = new SimulationSettings();
_simulation.OutputSchema = new OutputSchema();
_simulation.OutputSchema.AddInterval(new OutputInterval {
DomainHelperForSpecs.ConstantParameterWithValue(100).WithName(Constants.Parameters.END_TIME)
});
_simulation.Model = new OSPSuite.Core.Domain.Model {
Root = new Container()
};
_eventGroup = new EventGroup();
_application1 = new Container().WithName("App1").WithContainerType(ContainerType.Application);
_application1.Add(new MoleculeAmount().WithName(_compoundName));
_application1.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(Constants.Parameters.START_TIME));
_application2 = new Container().WithName("App2").WithContainerType(ContainerType.Application);
_application2.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(Constants.Parameters.START_TIME));
_application2.Add(new MoleculeAmount().WithName(_compoundName));
_simulation.Model.Root.Add(_eventGroup);
_eventGroup.Add(_application1);
_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])));
}