protected override void Context()
{
_globalPKAnalysisPresenter = A.Fake <IGlobalPKAnalysisPresenter>();
_concentrationDim = A.Fake <IDimension>();
_timeDim = A.Fake <IDimension>();
_view = A.Fake <IIndividualPKAnalysisView>();
_pkaAnalysisTask = A.Fake <IPKAnalysisTask>();
_simulation = A.Fake <IndividualSimulation>();
_simulations = new List <Simulation>();
_simulations.Add(_simulation);
_exportTask = A.Fake <IPKAnalysisExportTask>();
_individualPKAnalysisToDTOMapper = A.Fake <IIndividualPKAnalysisToPKAnalysisDTOMapper>();
_pkParameterRepository = A.Fake <IPKParameterRepository>();
;
var dataRepository = new DataRepository();
_baseGrid = new BaseGrid("Base", _timeDim);
_col1 = new DataColumn {
DataInfo = new DataInfo(ColumnOrigins.Calculation, AuxiliaryType.Undefined, "mg", DateTime.Now, string.Empty, string.Empty, 5), Dimension = _concentrationDim
};
_col2 = new DataColumn {
Dimension = _concentrationDim, DataInfo = new DataInfo(ColumnOrigins.Calculation, AuxiliaryType.Undefined, "mg", DateTime.Now, string.Empty, string.Empty, 5)
};
_col3 = new DataColumn {
Dimension = _concentrationDim, DataInfo = new DataInfo(ColumnOrigins.Calculation, AuxiliaryType.Undefined, "mg", DateTime.Now, string.Empty, string.Empty, 5)
};
dataRepository.Add(_col1);
dataRepository.Add(_col2);
_simulation.DataRepository = dataRepository;
var curve1 = A.Fake <Curve>();
A.CallTo(() => curve1.yData).Returns(_col1);
A.CallTo(() => curve1.xData).Returns(_baseGrid);
var curve2 = A.Fake <Curve>();
A.CallTo(() => curve2.yData).Returns(_col2);
A.CallTo(() => curve2.xData).Returns(_baseGrid);
var curve3 = A.Fake <Curve>();
A.CallTo(() => curve3.yData).Returns(_col3);
A.CallTo(() => curve3.xData).Returns(_col1);
_curves = new List <Curve> {
curve1, curve2, curve3
};
_allPKAnalysis = new List <Tuple <DataColumn, PKAnalysis> >();
_pkAnalysis1 = createPKAnalysis();
_pkAnalysis2 = createPKAnalysis();
_allPKAnalysis.Add(new Tuple <DataColumn, PKAnalysis>(_col1, _pkAnalysis1));
_allPKAnalysis.Add(new Tuple <DataColumn, PKAnalysis>(_col2, _pkAnalysis2));
_allGlobalPKParameters = new List <IParameter>();
A.CallTo(_pkaAnalysisTask).WithReturnType <IEnumerable <Tuple <DataColumn, PKAnalysis> > >().Returns(_allPKAnalysis);
A.CallTo(_pkaAnalysisTask).WithReturnType <IEnumerable <IParameter> >().Returns(_allGlobalPKParameters);
_presenterSettingsTask = A.Fake <IPresentationSettingsTask>();
sut = new IndividualPKAnalysisPresenter(_view, _pkaAnalysisTask, _exportTask, _globalPKAnalysisPresenter,
_individualPKAnalysisToDTOMapper, _pkParameterRepository, _presenterSettingsTask);
}
public static PKAnalysis GeneratePopulationAnalysis()
{
var analysis = new PKAnalysis();
analysis.AddChildren(new IEntity[]
{
new PKSimParameter {
Name = Constants.PKParameters.AUC, Value = 0.0
},
new PKSimParameter {
Name = Constants.PKParameters.AUC_inf, Value = 1.0
},
new PKSimParameter {
Name = Constants.PKParameters.C_max, Value = 2.0
},
new PKSimParameter {
Name = Constants.PKParameters.Tmax, Value = 3.0
},
new PKSimParameter {
Name = Constants.PKParameters.Thalf, Value = 4.0
},
new PKSimParameter {
Name = Constants.PKParameters.MRT, Value = 5.0
},
new PKSimParameter {
Name = Constants.PKParameters.FractionAucEndToInf, Value = 6.0
}
});
return(analysis);
}
protected override void Context()
{
base.Context();
//Simulate calculated results by setting the DataRepository
_aucIVSimulation = new IndividualSimulation {
DataRepository = _simulation.DataRepository
};
_pkAnalysis = new PKAnalysis();
_pkAnalysis.Add(DomainHelperForSpecs.ConstantParameterWithValue(2).WithName(Constants.PKParameters.AUC_inf));
A.CallTo(() => _globalPKAnalysisRunner.RunForBioavailability(_protocol, _simulation, _compound)).Returns(_aucIVSimulation);
A.CallTo(() => _pkAnalysisTask.CalculateFor(_aucIVSimulation, _venousBloodPlasma)).Returns(new IndividualPKAnalysis(_venousBloodPlasma, _pkAnalysis));
A.CallTo(() => _protocolFactory.Create(ProtocolMode.Simple, ApplicationTypes.Intravenous)).Returns(_protocol);
_protocol.AddParameter(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(Constants.Parameters.INFUSION_TIME));
_protocol.AddParameter(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.INPUT_DOSE));
_protocol.AddParameter(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(Constants.Parameters.START_TIME));
//single dosing
var schemaItem = A.Fake <SchemaItem>();
var inputDose = DomainHelperForSpecs.ConstantParameterWithValue(10);
var startTime = DomainHelperForSpecs.ConstantParameterWithValue(3);
A.CallTo(() => schemaItem.Dose).Returns(inputDose);
A.CallTo(() => schemaItem.StartTime).Returns(startTime);
_simulationSchemaItems.Add(schemaItem);
}
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 void addWarningsTo(PKAnalysis pkAnalysis, GlobalPKAnalysis globalPKAnalysis, string moleculeName)
{
if (globalPKAnalysis == null)
{
return;
}
addFractionAbsorbedWarningTo(pkAnalysis, globalPKAnalysis, moleculeName);
}
protected override void Context()
{
base.Context();
_pKAnalysis = PKAnalysisHelperForSpecs.GenerateIndividualPKAnalysis();
_dataTable = new DataTable();
_individualPKAnalyses = new List <IndividualPKAnalysis> {
new IndividualPKAnalysis(_dataColumn, _pKAnalysis)
};
A.CallTo(() => _individualPKAnalysisToDataTableMapper.MapFrom(_individualPKAnalyses, _curves, true)).Returns(_dataTable);
}
protected override void Context()
{
base.Context();
_simulation = new IndividualSimulation {
DataRepository = new DataRepository()
};
_baseGrid = new BaseGrid("Time", DomainHelperForSpecs.TimeDimensionForSpecs())
{
Values = new[] { 10f, 20f, 30f }
};
_dataColumn1 = new DataColumn("C1", DomainHelperForSpecs.ConcentrationDimensionForSpecs(), _baseGrid)
{
DataInfo = { Origin = ColumnOrigins.Calculation },
QuantityInfo = { Path = new[] { "C1", "Concentration" } },
Values = new[] { 11f, 21f, 31f }
};
_dataColumn2 = new DataColumn("C2", DomainHelperForSpecs.ConcentrationDimensionForSpecs(), _baseGrid)
{
DataInfo = { Origin = ColumnOrigins.Calculation },
QuantityInfo = { Path = new[] { "C2", "Concentration" } },
Values = new[] { 12f, 22f, 32f }
};
_simulation.DataRepository.Add(_dataColumn1);
_simulation.DataRepository.Add(_dataColumn2);
//Setup global PK analysis
_globalPKAnalysis = new GlobalPKAnalysis();
var c1Container = new Container().WithName("C1");
c1Container.Add(DomainHelperForSpecs.ConstantParameterWithValue(0.5).WithName(CoreConstants.PKAnalysis.FractionAbsorbed));
var c2Container = new Container().WithName("C2");
c2Container.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.PKAnalysis.FractionAbsorbed));
_globalPKAnalysis.Add(c1Container);
_globalPKAnalysis.Add(c2Container);
_pkC1 = new PKAnalysis
{
DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(Constants.PKParameters.MRT),
DomainHelperForSpecs.ConstantParameterWithValue(2).WithName(Constants.PKParameters.Tmax)
};
_pkC2 = new PKAnalysis
{
DomainHelperForSpecs.ConstantParameterWithValue(3).WithName(Constants.PKParameters.MRT),
DomainHelperForSpecs.ConstantParameterWithValue(4).WithName(Constants.PKParameters.Tmax)
};
A.CallTo(() => _pkMapper.MapFrom(_dataColumn1, A <PKValues> ._, A <PKParameterMode> ._, "C1")).Returns(_pkC1);
A.CallTo(() => _pkMapper.MapFrom(_dataColumn2, A <PKValues> ._, A <PKParameterMode> ._, "C2")).Returns(_pkC2);
_defaultNumberOfRules = DomainHelperForSpecs.ConstantParameterWithValue(3).Rules.Count;
}
protected override void Context()
{
base.Context();
_ddiRatioSimulation = new IndividualSimulation();
//Simulate calculated results by setting the DataRepository
_ddiRatioSimulation.DataRepository = _simulation.DataRepository;
_pkAnalysis = new PKAnalysis();
_pkAnalysis.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(Constants.PKParameters.C_max));
_pkAnalysis.Add(DomainHelperForSpecs.ConstantParameterWithValue(2).WithName(Constants.PKParameters.AUC_inf));
A.CallTo(() => _globalPKAnalysisRunner.RunForDDIRatio(_simulation)).Returns(_ddiRatioSimulation);
A.CallTo(() => _pkAnalysisTask.CalculateFor(_ddiRatioSimulation, _peripheralVenousBloodPlasma)).Returns(new IndividualPKAnalysis(_peripheralVenousBloodPlasma, _pkAnalysis));
}
private void addFractionAbsorbedWarningTo(PKAnalysis pkAnalysis, GlobalPKAnalysis globalPKAnalysis, string moleculeName)
{
var fractionAbsorbed = globalPKAnalysis.PKParameter(moleculeName, CoreConstants.PKAnalysis.FractionAbsorbed);
if (fractionAbsorbed == null)
{
return;
}
if (ValueComparer.AreValuesEqual(fractionAbsorbed.Value, 1, CoreConstants.DOUBLE_RELATIVE_EPSILON))
{
return;
}
addWarningsTo(pkAnalysis, PKSimConstants.Warning.FractionAbsorbedSmallerThanOne, CoreConstants.PKAnalysis.AllParametersInfluencedByFractionAbsorbed);
}
protected override void Context()
{
base.Context();
//Simulate calculated results by setting the DataRepository
_ddiRatioSimulation = new IndividualSimulation {
DataRepository = _simulation.DataRepository
};
_pkAnalysis = new PKAnalysis
{
DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(Constants.PKParameters.C_max_tDLast_tDEnd),
DomainHelperForSpecs.ConstantParameterWithValue(2).WithName(Constants.PKParameters.AUC_inf_tDLast)
};
A.CallTo(() => _globalPKAnalysisRunner.RunForDDIRatio(_simulation)).Returns(_ddiRatioSimulation);
A.CallTo(() => _pkAnalysisTask.CalculateFor(_ddiRatioSimulation, _peripheralVenousBloodPlasma)).Returns(new IndividualPKAnalysis(_peripheralVenousBloodPlasma, _pkAnalysis));
//multiple dosing
_simulationSchemaItems.AddRange(new[] { new SchemaItem(), new SchemaItem() });
}
protected void AddPKParameterToDataTable(PKAnalysis pkAnalysis, DataTable dataTable, string curveName, IParameter parameter, bool addMetaData)
{
var pkValue = parameter.ValueInDisplayUnit;
var row = dataTable.NewRow();
row[PKSimConstants.PKAnalysis.Value] = pkValue;
row[PKSimConstants.PKAnalysis.CurveName] = curveName;
if (addMetaData)
{
row[PKSimConstants.PKAnalysis.Compound] = parameter.ParentContainer.Name;
row[PKSimConstants.PKAnalysis.ParameterName] = parameter.Name;
row[PKSimConstants.PKAnalysis.Description] = descriptionFor(parameter);
row[PKSimConstants.PKAnalysis.Warning] = parameter.Validate().Message;
}
row[PKSimConstants.PKAnalysis.ParameterDisplayName] = _pkParameterRepository.DisplayNameFor(parameter.Name);
row[PKSimConstants.PKAnalysis.Unit] = parameter.DisplayUnit.Name;
dataTable.Rows.Add(row);
}
protected override void Context()
{
_exportTask = A.Fake <IPKAnalysisExportTask>();
_pkAnalysesTask = A.Fake <IPKAnalysesTask>();
_view = A.Fake <IPopulationPKAnalysisView>();
_populationPKAnalysisToDTOMapper = A.Fake <IPopulationPKAnalysisToPKAnalysisDTOMapper>();
_populationPKAnalysisToDataTableMapper = A.Fake <IPopulationPKAnalysisToDataTableMapper>();
_pkParameterRepository = A.Fake <IPKParameterRepository>();
_presenterSettingsTask = A.Fake <IPresentationSettingsTask>();
sut = new PopulationPKAnalysisPresenter(_view, _pkAnalysesTask, _exportTask, _populationPKAnalysisToDTOMapper, _pkParameterRepository, _presenterSettingsTask);
_populationDataCollector = A.Fake <IPopulationDataCollector>();
_timeProfileChartData = new ChartData <TimeProfileXValue, TimeProfileYValue>(null, null);
var pane = new PaneData <TimeProfileXValue, TimeProfileYValue>(null)
{
Caption = "TOTO"
};
_curve1 = new TimeProfileCurveData {
Caption = "A", Pane = pane
};
_curve2 = new TimeProfileCurveData {
Caption = "B", Pane = pane
};
_pk1 = new PKAnalysis();
_pk2 = new PKAnalysis();
_allPKanalysis = new List <PopulationPKAnalysis>
{
new PopulationPKAnalysis(_curve1, _pk1),
new PopulationPKAnalysis(_curve2, _pk2),
};
A.CallTo(() => _pkAnalysesTask.CalculateFor(_populationDataCollector, _timeProfileChartData)).Returns(_allPKanalysis);
A.CallTo(() => _view.BindTo(A <PKAnalysisDTO> ._)).Invokes(x => _dataTable = x.GetArgument <PKAnalysisDTO>(0).DataTable);
A.CallTo(() => _populationPKAnalysisToDataTableMapper.MapFrom(A <IReadOnlyList <PopulationPKAnalysis> > ._, true)).Returns(_dataTable);
}
public static PKAnalysis GenerateIndividualPKAnalysis()
{
var newPKAnalysis = new PKAnalysis();
newPKAnalysis.AddChildren(new IEntity[]
{
new PKSimParameter {
Name = Constants.PKParameters.AUC, Value = 0.0
},
new PKSimParameter {
Name = Constants.PKParameters.AUC_norm, Value = 1.0
},
new PKSimParameter {
Name = Constants.PKParameters.AUC_inf, Value = 2.0
},
new PKSimParameter {
Name = Constants.PKParameters.AUC_inf_norm, Value = 3.0
},
new PKSimParameter {
Name = Constants.PKParameters.C_max, Value = 4.0
},
new PKSimParameter {
Name = Constants.PKParameters.C_max_norm, Value = 5.0
},
new PKSimParameter {
Name = Constants.PKParameters.FractionAucEndToInf, Value = 6.0
},
new PKSimParameter {
Name = Constants.PKParameters.Tmax, Value = 7.0
},
new PKSimParameter {
Name = Constants.PKParameters.Thalf, Value = 8.0
},
new PKSimParameter {
Name = Constants.PKParameters.MRT, Value = 9.0
}
});
return(newPKAnalysis);
}
protected void AddPKParametersToDataTable(PKAnalysis pkAnalysis, DataTable dataTable, string curveName, bool addMetaData)
{
pkAnalysis.AllPKParameters.Each(parameter => AddPKParameterToDataTable(pkAnalysis, dataTable, curveName, parameter, addMetaData));
}
public PopulationPKAnalysis(CurveData <TimeProfileXValue, TimeProfileYValue> curveData, PKAnalysis pkAnalysis)
{
CurveData = curveData;
PKAnalysis = pkAnalysis;
}
protected override void Because()
{
_result = sut.MapFrom(_col, _pkValues, _mode, _drugName);
}
private void addWarningsTo(PKAnalysis pkAnalysis, string warning, IEnumerable <string> parameterNames)
{
parameterNames.Select(pkAnalysis.Parameter)
.Where(p => p != null)
.Each(p => p.Rules.Add(warningRule(warning)));
}
private double?pkParameterValue(PKAnalysis pkAnalysis, string pkParameterName)
{
var parameter = pkAnalysis.Parameter(pkParameterName);
return(parameter?.Value);
}
public IndividualPKAnalysis(DataColumn dataColumn, PKAnalysis pkAnalysis)
{
DataColumn = dataColumn;
PKAnalysis = pkAnalysis;
}
