public static PivotResult CreatePivotResult(PopulationPivotAnalysis pivotAnalysis, Aggregate aggregate,
PopulationAnalysisCovariateField genderFielder,
PopulationAnalysisCovariateField raceField,
PopulationAnalysisParameterField bmiField,
PopulationAnalysisPKParameterField cmaxField)
{
var pivotResultCreator = new PivotResultCreator(new Pivoter(), new PopulationAnalysisFlatTableCreator());
var populationSimulation = A.Fake <IPopulationDataCollector>();
A.CallTo(() => populationSimulation.NumberOfItems).Returns(3);
//thin, thin, big
A.CallTo(() => populationSimulation.AllValuesFor(bmiField.ParameterPath)).Returns(new List <double> {
10, 20, 30
});
A.CallTo(() => populationSimulation.AllCovariateValuesFor(genderFielder.Covariate)).Returns(new List <string> {
"Male", "Female", "Male"
});
A.CallTo(() => populationSimulation.AllCovariateValuesFor(raceField.Covariate)).Returns(new List <string> {
"US", "EU", "EU"
});
A.CallTo(() => populationSimulation.AllPKParameterValuesFor(cmaxField.QuantityPath, cmaxField.PKParameter)).Returns(new List <double> {
900, 600, 1000
});
A.CallTo(() => populationSimulation.AllSimulationNames).Returns(new List <string> {
"Sim", "Sim", "Sim"
});
return(pivotResultCreator.Create(pivotAnalysis, populationSimulation, new ObservedDataCollection(), aggregate));
}
private QuantityPKParameter pkParameterFrom(PopulationAnalysisPKParameterField populationAnalysisPKParameterField)
{
if (populationAnalysisPKParameterField == null)
{
return(null);
}
return(PopulationDataCollector.PKParameterFor(populationAnalysisPKParameterField.QuantityPath, populationAnalysisPKParameterField.PKParameter));
}
protected override void Context()
{
base.Context();
_pkParameter = new QuantityPKParameter();
_populationPivotAnalysis = new PopulationPivotAnalysis();
_populationDataCollector = A.Fake <IPopulationDataCollector>();
_field = A.Fake <PopulationAnalysisPKParameterField>();
sut.StartAnalysis(_populationDataCollector, _populationPivotAnalysis);
}
protected override void Context()
{
base.Context();
_displayUnit = A.Fake <Unit>();
_mergedDimension = A.Fake <IDimension>();
_pkParameterDimension = A.Fake <IDimension>();
_pkParameter = new QuantityPKParameter().WithName("AUC").WithDimension(_pkParameterDimension);
_pkParameterField = new PopulationAnalysisPKParameterField().WithDimension(_pkParameterDimension);
_pkParameterField.DisplayUnit = _displayUnit;
A.CallTo(() => _dimensionRepository.MergedDimensionFor(A <NumericFieldContext> ._))
.Invokes(x => _numericFieldContect = x.GetArgument <NumericFieldContext>(0))
.Returns(_mergedDimension);
}
public override void GlobalContext()
{
base.GlobalContext();
_populationPivotAnalysis = new PopulationPivotAnalysis();
_pkParameterField = new PopulationAnalysisPKParameterField().WithName("PKParam");
_pkParameterField.PKParameter = "AUC";
_pkParameterField.QuantityPath = "A|B|C";
_parameterField = new PopulationAnalysisParameterField().WithName("Param");
_parameterField.ParameterPath = "A|B|C|D";
_populationPivotAnalysis.Add(_pkParameterField);
_populationPivotAnalysis.Add(_parameterField);
_populationPivotAnalysis.SetPosition(_parameterField, PivotArea.DataArea, 1);
_populationPivotAnalysis.SetPosition(_pkParameterField, PivotArea.RowArea, 2);
}
protected override async Task Context()
{
await base.Context();
_populationDataCollector = A.Fake <IPopulationDataCollector>();
_templatePopulationAnalysis = new PopulationPivotAnalysis();
_pkParameterFound = new PopulationAnalysisPKParameterField {
QuantityType = QuantityType.Drug, PKParameter = "AUC", QuantityPath = "P1"
};
_quantityNotFound = new PopulationAnalysisPKParameterField {
QuantityType = QuantityType.Drug, PKParameter = "AUC", QuantityPath = "P2"
};
_pkParameterNotFound = new PopulationAnalysisPKParameterField {
QuantityType = QuantityType.Metabolite, PKParameter = "AUC", QuantityPath = "P3"
};
_templatePopulationAnalysis.Add(_pkParameterFound);
_templatePopulationAnalysis.Add(_quantityNotFound);
_templatePopulationAnalysis.Add(_pkParameterNotFound);
_cache = new PathCacheForSpecs <IQuantity>
{
{ "P1", new MoleculeAmount {
QuantityType = QuantityType.Drug
} },
{ "Q2", new MoleculeAmount {
QuantityType = QuantityType.Drug
} },
{ "P3", new MoleculeAmount {
QuantityType = QuantityType.Metabolite
} }
};
A.CallTo(() => _populationDataCollector.HasPKParameterFor("P1", "AUC")).Returns(true);
A.CallTo(() => _populationDataCollector.HasPKParameterFor("P2", "AUC")).Returns(false);
A.CallTo(() => _populationDataCollector.HasPKParameterFor("P3", "AUC")).Returns(false);
A.CallTo(_templateTask).WithReturnType <Task <PopulationAnalysis> >().Returns(_templatePopulationAnalysis);
A.CallTo(() => _entitiesInContainerRetriever.OutputsFrom(_populationDataCollector)).Returns(_cache);
A.CallTo(_dialogCreator).WithReturnType <ViewResult>().Returns(ViewResult.Yes);
A.CallTo(() => _keyPathMapper.MapFrom(_pkParameterFound.QuantityPath, QuantityType.Drug, true)).Returns(new KeyPathMap("P1"));
A.CallTo(() => _keyPathMapper.MapFrom(_quantityNotFound.QuantityPath, QuantityType.Drug, true)).Returns(new KeyPathMap("QUANTITY NOT FOUND"));
A.CallTo(() => _keyPathMapper.MapFrom(_pkParameterNotFound.QuantityPath, QuantityType.Metabolite, true)).Returns(new KeyPathMap("P3"));
}
protected override void Context()
{
sut = new PopulationPivotAnalysis();
_pkField1 = new PopulationAnalysisPKParameterField {
PKParameter = "P1"
}.WithName("Field1");
_pkField2 = new PopulationAnalysisPKParameterField {
PKParameter = "P2"
}.WithName("Field2");
_paraField1 = new PopulationAnalysisParameterField {
ParameterPath = "Path3"
}.WithName("Field3");
_paraField2 = new PopulationAnalysisParameterField {
ParameterPath = "Path4"
}.WithName("Field4");
_derivedField1 = A.Fake <PopulationAnalysisDerivedField>().WithName("Field5");
sut.Add(_paraField1);
sut.Add(_paraField2);
sut.Add(_pkField1);
sut.Add(_pkField2);
sut.Add(_derivedField1);
}
private void mapPKParameterFieldToModel(PopulationAnalysisField snapshot, PopulationAnalysisPKParameterField field)
{
mapQuantityFieldToModel(snapshot, field);
field.PKParameter = snapshot.PKParameter;
}
public void Plot(IPopulationDataCollector populationDataCollector, QuantityPKParameter pkParameter, PopulationAnalysisPKParameterField pkParameterField)
{
plotContinousData(populationDataCollector, pkParameter, pkParameterField, x => x.Plot);
}
protected override Task Context()
{
_groupingDefinitionMapper = A.Fake <GroupingDefinitionMapper>();
_dimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
_mergedDimension = DomainHelperForSpecs.TimeDimensionForSpecs();
_unit = _mergedDimension.Unit("h"); // this unit is defined in the merged dimension but not in the field dimension
_dimensionRepository = A.Fake <IDimensionRepository>();
sut = new PopulationAnalysisFieldMapper(_groupingDefinitionMapper, _dimensionRepository);
_groupingItem1 = new GroupingItem();
_parameterField = new PopulationAnalysisParameterField
{
Name = "P",
ParameterPath = "A|B",
Scaling = Scalings.Linear,
Dimension = _dimension,
DisplayUnit = _unit
};
_pkParameterField = new PopulationAnalysisPKParameterField
{
Name = "PK",
Dimension = _dimension,
DisplayUnit = _unit,
PKParameter = "AUC",
QuantityPath = "A|B|C",
QuantityType = QuantityType.Observer | QuantityType.Drug
};
_outputField = new PopulationAnalysisOutputField
{
Name = "Output",
Dimension = _dimension,
DisplayUnit = _unit,
QuantityType = QuantityType.BaseGrid,
QuantityPath = "A|B|C",
Color = Color.AntiqueWhite
};
_groupingDefinition = new FixedLimitsGroupingDefinition("AA");
_groupingField = new PopulationAnalysisGroupingField(_groupingDefinition)
{
Name = "Grouping",
};
_covariateField = new PopulationAnalysisCovariateField
{
Name = "Gender",
Covariate = "Gender",
};
_covariateField.AddGroupingItem(_groupingItem1);
_snapshotGroupingDefinition = new Snapshots.GroupingDefinition();
A.CallTo(() => _groupingDefinitionMapper.MapToSnapshot(_groupingDefinition)).Returns(_snapshotGroupingDefinition);
A.CallTo(() => _dimensionRepository.DimensionByName(_dimension.Name)).Returns(_dimension);
A.CallTo(() => _dimensionRepository.MergedDimensionFor(A <INumericValueField> ._)).Returns(_mergedDimension);
return(_completed);
}
protected override async Task Because()
{
_newPKParameterField = await sut.MapToModel(_snapshot, new SnapshotContext()) as PopulationAnalysisPKParameterField;
}
protected override void Because()
{
_result = sut.CreateFor(_pkParameter, QuantityType.Metabolite, "quantityPath");
}
public PKParameterFieldSelectedEventArgs(QuantityPKParameter pkParameter, PopulationAnalysisPKParameterField pkParameterField) : base(pkParameter)
{
PKParameterField = pkParameterField;
}
private void drawDistributionFor(QuantityPKParameter pkParameter, PopulationAnalysisPKParameterField populationAnalysisPKParameterField)
{
_populationAnalysisFieldDistributionPresenter.Plot(_populationDataCollector, pkParameter, populationAnalysisPKParameterField);
}
public override void GlobalContext()
{
base.GlobalContext();
_populationAnalysis = new PopulationPivotAnalysis();
_pkParameterField = new PopulationAnalysisPKParameterField().WithName("PKParam");
_pkParameterField.PKParameter = "AUC";
_pkParameterField.QuantityPath = "A|B|C";
_pkParameterField.QuantityType = QuantityType.Drug;
_pkParameterField.Dimension = _dimensionRepository.MassConcentration;
_parameterField = new PopulationAnalysisParameterField().WithName("Param");
_parameterField.ParameterPath = "A|B|C|D";
_parameterField.Dimension = _dimensionRepository.Auc;
_outputField = new PopulationAnalysisOutputField().WithName("Output");
_outputField.QuantityPath = "A|B|C";
_outputField.Dimension = _dimensionRepository.Auc;
_outputField.Color = Color.Aquamarine;
_genderField = new PopulationAnalysisCovariateField {
Covariate = "Gender"
}.WithName("Gender");
var numberOfBinsGroupingDefinition = new NumberOfBinsGroupingDefinition(_parameterField.Name)
{
NumberOfBins = 2
};
numberOfBinsGroupingDefinition.NamingPattern = "AA";
numberOfBinsGroupingDefinition.StartColor = Color.AliceBlue;
numberOfBinsGroupingDefinition.EndColor = Color.RoyalBlue;
numberOfBinsGroupingDefinition.Strategy = LabelGenerationStrategies.Roman;
numberOfBinsGroupingDefinition.AddItems(PopulationAnalysisHelperForSpecs.BMIGroups);
_numberOfBinsDerivedField = new PopulationAnalysisGroupingField(numberOfBinsGroupingDefinition).WithName("NumberOfBins");
var fixedLimitsGroupingDefinition = new FixedLimitsGroupingDefinition(_pkParameterField.Name);
fixedLimitsGroupingDefinition.AddItems(PopulationAnalysisHelperForSpecs.AgeGroups);
_fixedLimitsGroupingDefinitionField = new PopulationAnalysisGroupingField(fixedLimitsGroupingDefinition)
.WithName("FixedLimits");
fixedLimitsGroupingDefinition.SetLimits(new[] { 1d, 2d }.OrderBy(x => x));
_derivedFieldWithFixedExpression = new PopulationAnalysisExpressionField("A+B")
.WithName("FixedExpression");
var valueMappingGroupingDefinition = new ValueMappingGroupingDefinition(_genderField.Name);
valueMappingGroupingDefinition.AddValueLabel("Male", PopulationAnalysisHelperForSpecs.GroupingItemMale);
valueMappingGroupingDefinition.AddValueLabel("Female", PopulationAnalysisHelperForSpecs.GroupingItemFemale);
var valueMappingGroupingDefinitionField = new PopulationAnalysisGroupingField(valueMappingGroupingDefinition).WithName("ValueMapping");
_populationAnalysis.Add(_pkParameterField);
_populationAnalysis.Add(_parameterField);
_populationAnalysis.Add(_genderField);
_populationAnalysis.Add(_numberOfBinsDerivedField);
_populationAnalysis.Add(_fixedLimitsGroupingDefinitionField);
_populationAnalysis.Add(_derivedFieldWithFixedExpression);
_populationAnalysis.Add(valueMappingGroupingDefinitionField);
_populationAnalysis.Add(_outputField);
}
protected override void Context()
{
base.Context();
_populationSimulation = new PopulationSimulation {
SimulationSettings = new SimulationSettings {
OutputSelections = new OutputSelections()
}
};
var liverCellsDrugConc = "Liver|Cells|Drug|Conc";
_populationSimulation.OutputSelections.AddOutput(new QuantitySelection(liverCellsDrugConc, QuantityType.Drug));
_populationSimulation.OutputSelections.AddOutput(new QuantitySelection("Liver|Plasma|Drug|Conc", QuantityType.Drug));
_populationStatisticalAnalysis = new PopulationStatisticalAnalysis();
_timeProfileAnalysis = new TimeProfileAnalysisChart {
PopulationAnalysis = _populationStatisticalAnalysis
};
_outputField1 = new PopulationAnalysisOutputField {
QuantityPath = "Kidney|Cell|Drug|Conc", Name = "outputField1"
};
_derivedField1 = new PopulationAnalysisGroupingField(new NumberOfBinsGroupingDefinition(_outputField1.Name))
{
Name = "derivedField1"
};
_outputField2 = new PopulationAnalysisOutputField {
QuantityPath = liverCellsDrugConc, Name = "outputField2"
};
_derivedField2 = new PopulationAnalysisGroupingField(new NumberOfBinsGroupingDefinition(_outputField2.Name))
{
Name = "derivedField2"
};
_pkField1 = new PopulationAnalysisPKParameterField {
QuantityPath = "Kidney|Cell|Drug|Conc", Name = "pkField1"
};
_pkDerivedField1 = new PopulationAnalysisGroupingField(new NumberOfBinsGroupingDefinition(_pkField1.Name))
{
Name = "pkDerivedField1"
};
_pkField2 = new PopulationAnalysisPKParameterField {
QuantityPath = liverCellsDrugConc, Name = "pkField2"
};
_pkDerivedField2 = new PopulationAnalysisGroupingField(new NumberOfBinsGroupingDefinition(_pkField2.Name))
{
Name = "pkDerivedField2"
};
_populationStatisticalAnalysis.Add(_outputField1);
_populationStatisticalAnalysis.Add(_outputField2);
_populationStatisticalAnalysis.Add(_derivedField1);
_populationStatisticalAnalysis.Add(_derivedField2);
_populationStatisticalAnalysis.Add(_pkField1);
_populationStatisticalAnalysis.Add(_pkField2);
_populationStatisticalAnalysis.Add(_pkDerivedField1);
_populationStatisticalAnalysis.Add(_pkDerivedField2);
_populationSimulation.AddAnalysis(_timeProfileAnalysis);
}
