protected override void Context()
{
base.Context();
_userDefinedPKParameter = new UserDefinedPKParameter {
Name = "MyParam"
};
}
public override void GlobalContext()
{
base.GlobalContext();
var simulationFile = HelperForSpecs.DataFile("S1.pkml");
var simulationPersister = Api.GetSimulationPersister();
var pkParametersTask = Api.GetPKParameterTask();
_simulation = simulationPersister.LoadSimulation(simulationFile);
_sensitivityAnalysis = new SensitivityAnalysis(_simulation)
{
NumberOfSteps = 2, VariationRange = 0.2
};
//Should calculate CMax/100
_userDefinedPKParameter = new UserDefinedPKParameter {
Name = "Toto", NormalizationFactor = 100, StandardPKParameter = StandardPKParameter.C_max
};
pkParametersTask.AddUserDefinedPKParameter(_userDefinedPKParameter);
_userDefinedCLParameter = new UserDefinedPKParameter {
Name = "MyCL", StandardPKParameter = StandardPKParameter.CL
};
pkParametersTask.AddUserDefinedPKParameter(_userDefinedCLParameter);
var containerTask = Api.GetContainerTask();
var liverVolumes = containerTask.AllParametersMatching(_simulation, "Organism|Liver|Volume");
_sensitivityAnalysis.AddParameterPaths(liverVolumes.Select(x => x.ConsolidatedPath()));
}
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 void RemoveUserDefinedPKParameter(UserDefinedPKParameter userDefinedPKParameter)
{
if (userDefinedPKParameter == null)
{
return;
}
_pkParameterRepository.Remove(userDefinedPKParameter);
}
protected override void Context()
{
base.Context();
_result = _simulationRunner.Run(new SimulationRunArgs {
Simulation = _simulation
});
_userDefinedPKParameter =
_pkParameterTask.CreateUserDefinedPKParameter("MyCmax", StandardPKParameter.C_max, displayName: null, displayUnit: "mg/l");
_pkParameterTask.AddUserDefinedPKParameter(_userDefinedPKParameter);
}
public void AddUserDefinedPKParameter(UserDefinedPKParameter userDefinedPKParameter)
{
var existingUserDefinedPKParameter = UserDefinedPKParameterByName(userDefinedPKParameter.Name);
if (existingUserDefinedPKParameter != null)
{
_logger.AddWarning(Warning.UserDefinedPKParameterAlreadyExistsAndWillBeReplaced(userDefinedPKParameter.Name));
return;
}
_pkParameterRepository.Add(userDefinedPKParameter);
}
public override void GlobalContext()
{
base.GlobalContext();
_multipleDosingColumn = DataColumnLoader.GetDataColumnFrom("MultipleDosing_0_8_16");
_pkOptions = new PKCalculationOptions
{
TotalDrugMassPerBodyWeight = 10,
};
_pkOptions.AddInterval(new DosingInterval {
StartValue = 0, EndValue = 8, DrugMassPerBodyWeight = _firstDose
});
_pkOptions.AddInterval(new DosingInterval {
StartValue = 8, EndValue = 16, DrugMassPerBodyWeight = _oneMinusLastDose
});
_pkOptions.AddInterval(new DosingInterval {
StartValue = 16, EndValue = 48, DrugMassPerBodyWeight = _lastDose
});
_cmax_tD1_tD2 = new UserDefinedPKParameter {
StartApplicationIndex = 0, EndApplicationIndex = 1, StandardPKParameter = StandardPKParameter.C_max, Name = "MyCmaxD1D2"
};
_cmax_tD1_tD2_DOSE_BW = new UserDefinedPKParameter {
StartApplicationIndex = 0, EndApplicationIndex = 1, StandardPKParameter = StandardPKParameter.C_max, Name = "MyCmaxD1D2_Normalized", NormalizationFactor = _firstDose
};
_cmax_tD1_tD2_DOSE_BW_auto = new UserDefinedPKParameter {
StartApplicationIndex = 0, EndApplicationIndex = 1, StandardPKParameter = StandardPKParameter.C_max_norm, Name = "MyCmaxD1D2_Normalized_auto"
};
_tmax_tD1_tD2 = new UserDefinedPKParameter {
StartApplicationIndex = 0, EndApplicationIndex = 1, StandardPKParameter = StandardPKParameter.t_max, Name = "MyTmaxD1D2"
};
_cmax_t1_t2 = new UserDefinedPKParameter {
StartTime = 0, EndTime = 8, StandardPKParameter = StandardPKParameter.C_max, Name = "MyCmaxT1T2"
};
_cmax_t1_t2_offset = new UserDefinedPKParameter {
StartTime = 0, StartTimeOffset = 16, EndTime = 48, StandardPKParameter = StandardPKParameter.C_max, Name = "MyCmaxT1T2offset"
};
_cmax_t1_offset_no_end = new UserDefinedPKParameter {
StartTime = 0, StartTimeOffset = 16, StandardPKParameter = StandardPKParameter.C_max, Name = "MyCmaxT1offset_no_end"
};
_tThreshold = new UserDefinedPKParameter {
StartApplicationIndex = 0, StandardPKParameter = StandardPKParameter.Tthreshold, Name = "Threshold", ConcentrationThreshold = 4
};
_tThreshold_last = new UserDefinedPKParameter {
StartApplicationIndex = 2, StandardPKParameter = StandardPKParameter.Tthreshold, Name = "Threshold_last", ConcentrationThreshold = 5
};
_allDynamicPkParameters = new[] { _cmax_tD1_tD2, _tmax_tD1_tD2, _cmax_t1_t2, _cmax_t1_t2_offset, _cmax_t1_offset_no_end, _cmax_tD1_tD2_DOSE_BW, _tThreshold, _tThreshold_last, _cmax_tD1_tD2_DOSE_BW_auto };
}
public UserDefinedPKParameter CreateUserDefinedPKParameter(
string name,
StandardPKParameter standardPKParameter,
string displayName,
string displayUnit)
{
var defaultDimension = _dimensionTask.DimensionForStandardPKParameter(standardPKParameter);
var userDefinedPKParameters = new UserDefinedPKParameter
{
Name = name,
DisplayName = displayName,
Dimension = defaultDimension,
DisplayUnit = displayUnit,
StandardPKParameter = standardPKParameter
};
//No display unit defined, we return the user defined pk parameter
if (string.IsNullOrEmpty(displayUnit))
{
return(userDefinedPKParameters);
}
var dimensionForDisplayUnit = _dimensionTask.DimensionForUnit(displayUnit);
//Display unit belongs to the dimension. We can use this
if (Equals(defaultDimension, dimensionForDisplayUnit))
{
return(userDefinedPKParameters);
}
//We have two dimensions. Do we have a converter between those dimensions?
if (_dimensionFactory.HasMergingInformation(defaultDimension, dimensionForDisplayUnit))
{
return(userDefinedPKParameters);
}
//There is no converter defined between those dimensions.
//We use the dimension defined for the display unit or create a user defined dimension otherwise
userDefinedPKParameters.Dimension = dimensionForDisplayUnit ?? _dimensionFactory.CreateUserDefinedDimension(name, displayUnit);
return(userDefinedPKParameters);
}
protected override void Because()
{
_userDefinedParameter = sut.CreateUserDefinedPKParameter("Test", StandardPKParameter.C_trough, "Test", "not_there");
}