protected override void Context()
{
base.Context();
_populationSimulationComparison = new PopulationSimulationComparison();
_simulationNameField = new PopulationAnalysisCovariateField();
A.CallTo(() => _populationAnalysisFieldFactory.CreateFor(CoreConstants.Covariates.SIMULATION_NAME, _populationSimulationComparison)).Returns(_simulationNameField);
}
protected override void Context()
{
_dimensionRepository = A.Fake <IDimensionRepository>();
_representationInfoRepository = A.Fake <IRepresentationInfoRepository>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
_observedcurveDataMapper = A.Fake <IDataRepositoryToObservedCurveDataMapper>();
_statisticalAnalysis = new PopulationStatisticalAnalysis();
_genderField = ChartDataHelperForSpecs.CreateGenderField();
_statisticalAnalysis.Add(_genderField);
_statisticalAnalysis.Add(_outputFieldVenousBloodPlasma);
_statisticalAnalysis.Add(_outputFieldLiverCell);
_predefinedStatisticalAggregation = new PredefinedStatisticalAggregation {
Selected = true
};
_percentileStatisticalAggregation = new PercentileStatisticalAggregation {
Selected = false, Percentile = 50
};
_statisticalAnalysis.AddStatistic(_predefinedStatisticalAggregation);
_statisticalAnalysis.AddStatistic(_percentileStatisticalAggregation);
A.CallTo(() => _representationInfoRepository.DisplayNameFor(_predefinedStatisticalAggregation)).Returns(_singlecurveId);
A.CallTo(() => _representationInfoRepository.DisplayNameFor(_percentileStatisticalAggregation)).Returns(_percentileId);
_statisticalDataCalculator = new StatisticalDataCalculator();
_pivotResultCreator = A.Fake <IPivotResultCreator>();
sut = new TimeProfileChartDataCreator(_dimensionRepository, _pivotResultCreator, _representationInfoRepository,
_statisticalDataCalculator, _lazyLoadTask, _observedcurveDataMapper);
}
protected override void Context()
{
base.Context();
var populationFieldFactory = A.Fake <PopulationAnalysisFieldFactory>();
_covariateField = populationFieldFactory.CreateFor("Gender", _populationDataCollector);
_populationAnalysis.Add(_covariateField);
_genderValues = new string[] { "Male", "Female" };
_covariateField.AddGroupingItem(new GroupingItem {
Label = "Male", Color = PKSimColors.Male, Symbol = Symbols.Circle
});
_covariateField.AddGroupingItem(new GroupingItem {
Label = "Female", Color = PKSimColors.Female, Symbol = Symbols.Diamond
});
var referenceSimulation = A.Fake <PopulationSimulation>().WithName("Sim");
_referenceGroupingItem = new GroupingItem {
Label = "Reference", Color = Color.Black, Symbol = Symbols.Circle
};
_populationDataCollector.ReferenceSimulation = referenceSimulation;
_populationDataCollector.ReferenceGroupingItem = _referenceGroupingItem;
A.CallTo(() => _populationDataCollector.NumberOfItems).Returns(_ageValues.Count * 2);
A.CallTo(() => _populationDataCollector.AllSimulationNames()).Returns(
Enumerable.Repeat(referenceSimulation.Name, _ageValues.Count).Concat(
Enumerable.Repeat("Sim2", _ageValues.Count)).ToArray());
A.CallTo(() => _populationDataCollector.AllValuesFor(_ageField.ParameterPath)).Returns(_ageValues.Concat(_ageValues).ToArray());
A.CallTo(() => _populationDataCollector.AllCovariateValuesFor(_covariateField.Covariate)).Returns(_genderValues.Concat(_genderValues).Concat(_genderValues).ToArray());
}
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));
}
protected override void Context()
{
base.Context();
_pivotAnalysis = new PopulationPivotAnalysis();
_field = new PopulationAnalysisCovariateField().WithName("Param");
_pivotAnalysis.Add(_field);
}
protected override void Because()
{
_covariate = sut.CreateFor(_covariateName, _populationDataCollector);
_covariate.ReferenceGroupingItem = new GroupingItem()
{
Color = Color.Black, Label = _referenceLabel, Symbol = Symbols.Circle
};
}
public void Plot(IPopulationDataCollector populationDataCollector, PopulationAnalysisCovariateField covariateField)
{
var fields = new List <IPopulationAnalysisField> {
covariateField
};
plotDiscreteData(populationDataCollector, fields, covariateField);
}
protected override void Context()
{
base.Context();
_pivotAnalysis = new PopulationPivotAnalysis();
_parameterField = new PopulationAnalysisCovariateField().WithName("Param");
_dataArea = new PopulationAnalysisParameterField().WithName("OnFilter");
_pivotAnalysis.Add(_parameterField);
_pivotAnalysis.Add(_dataArea);
_pivotAnalysis.SetPosition(_dataArea, PivotArea.DataArea, 0);
}
protected override void Context()
{
base.Context();
_covriateName = "Gender";
_covariateField = new PopulationAnalysisCovariateField().WithName(_covriateName);
A.CallTo(() => _populationAnalysisFieldFactory.CreateFor(_covriateName, _populationDataCollector)).Returns(_covariateField);
_dataTable = new DataTable();
_dataTable.AddColumn <string>(_covriateName);
A.CallTo(_flatTableCreator).WithReturnType <DataTable>().Returns(_dataTable);
}
protected override void Context()
{
base.Context();
_pivotAnalysis = new PopulationPivotAnalysis();
_parameterField = new PopulationAnalysisCovariateField().WithName("Param");
_existingColorField = new PopulationAnalysisCovariateField().WithName("ColorField");
_filterArea = new PopulationAnalysisParameterField().WithName("OnFilter");
_pivotAnalysis.Add(_parameterField);
_pivotAnalysis.Add(_existingColorField);
_pivotAnalysis.Add(_filterArea);
_pivotAnalysis.SetPosition(_filterArea, PivotArea.FilterArea, 0);
_pivotAnalysis.ColorField = _existingColorField;
}
private void addCovariateField(PopulationAnalysisCovariateField covariateField)
{
if (!hasReferenceSimulation)
{
addDataField(covariateField);
}
else
{
var covariateFieldInternalName = ShortGuid.NewGuid().ToString();
_allCovariateFields.Add(covariateField.Name, covariateFieldInternalName);
addDataField(covariateField, covariateFieldInternalName);
}
}
protected override void Context()
{
_view = A.Fake <IValueMappingGroupingView>();
_colorGenerator = A.Fake <IColorGenerator>();
_symbolGenerator = A.Fake <ISymbolGenerator>();
sut = new ValueMappingGroupingPresenter(_view, _colorGenerator, _symbolGenerator);
_populationDataCollector = A.Fake <IPopulationDataCollector>();
_covariateField = A.Fake <PopulationAnalysisCovariateField>();
A.CallTo(() => _covariateField.GetValues(_populationDataCollector)).Returns(new[] { "Male", "Male", "Female", "Female" });
A.CallTo(() => _view.BindTo(A <IEnumerable <GroupingLabelDTO> > ._))
.Invokes(x => _allLabels = x.GetArgument <IEnumerable <GroupingLabelDTO> >(0).ToList());
}
protected override void Context()
{
_dimensionRepository = A.Fake <IDimensionRepository>();
_representationInfoRepository = A.Fake <IRepresentationInfoRepository>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
_observedCurveDataMapper = A.Fake <IDataRepositoryToObservedCurveDataMapper>();
_statisticalAnalysis = new PopulationStatisticalAnalysis();
_genderField = ChartDataHelperForSpecs.CreateGenderField();
_statisticalAnalysis.Add(_genderField);
_statisticalAnalysis.Add(_outputFieldVenousBloodPlasma);
_statisticalAnalysis.Add(_outputFieldLiverCell);
_predefinedStatisticalAggregation = new PredefinedStatisticalAggregation {
Selected = true
};
_percentileStatisticalAggregation = new PercentileStatisticalAggregation {
Selected = false, Percentile = 50
};
_statisticalAnalysis.AddStatistic(_predefinedStatisticalAggregation);
_statisticalAnalysis.AddStatistic(_percentileStatisticalAggregation);
A.CallTo(() => _representationInfoRepository.DisplayNameFor(_predefinedStatisticalAggregation)).Returns(_singleCurveId);
A.CallTo(() => _representationInfoRepository.DisplayNameFor(_percentileStatisticalAggregation)).Returns(_percentileId);
_statisticalDataCalculator = new StatisticalDataCalculator();
_pivotResultCreator = A.Fake <IPivotResultCreator>();
_mergedDimensionVenousBloodPlasma = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
_mergedDimensionLiverCell = DomainHelperForSpecs.FractionDimensionForSpecs();
A.CallTo(() => _dimensionRepository.MergedDimensionFor(A <IWithDimension> ._))
.WhenArgumentsMatch((IWithDimension context) => Equals((context as NumericFieldContext)?.NumericValueField, _outputFieldVenousBloodPlasma))
.Returns(_mergedDimensionVenousBloodPlasma);
A.CallTo(() => _dimensionRepository.MergedDimensionFor(A <IWithDimension> ._))
.WhenArgumentsMatch((IWithDimension context) => Equals((context as NumericFieldContext)?.NumericValueField, _outputFieldLiverCell))
.Returns(_mergedDimensionLiverCell);
sut = new TimeProfileChartDataCreator(_dimensionRepository, _pivotResultCreator, _representationInfoRepository,
_statisticalDataCalculator, _lazyLoadTask, _observedCurveDataMapper);
}
protected override void Context()
{
base.Context();
_populationDataCollector = A.Fake <IPopulationDataCollector>();
_templatePopulationAnalysis = new PopulationPivotAnalysis();
_covariateFound = new PopulationAnalysisCovariateField {
Covariate = "Covariate1"
};
_covariateNotFound = new PopulationAnalysisCovariateField {
Covariate = "Covariate2"
};
_templatePopulationAnalysis.Add(_covariateFound);
_templatePopulationAnalysis.Add(_covariateNotFound);
A.CallTo(_templateTask).WithReturnType <PopulationAnalysis>().Returns(_templatePopulationAnalysis);
A.CallTo(() => _populationDataCollector.AllCovariateNames).Returns(new List <string> {
_covariateFound.Covariate
});
A.CallTo(_dialogCreator).WithReturnType <ViewResult>().Returns(ViewResult.Yes);
}
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();
_covariateField = A.Fake <PopulationAnalysisCovariateField>();
sut.StartAnalysis(_populationDataCollector, _populationPivotAnalysis);
}
public CovariateFieldSelectedEventArgs(string covariate, PopulationAnalysisCovariateField covariateField)
{
Covariate = covariate;
CovariateField = covariateField;
}
public static PivotResult CreateOutputResults(PopulationPivotAnalysis analysis, PopulationAnalysisCovariateField genderField, PopulationAnalysisOutputField outputField1,
PopulationAnalysisOutputField outputField2,
ObservedDataCollection observedDataCollection = null)
{
var populationSimulation = A.Fake <IPopulationDataCollector>();
var pivotResultCreator = new PivotResultCreator(new Pivoter(), new PopulationAnalysisFlatTableCreator());
//simulation with 4 time points
var time = new QuantityValues {
Values = new float[] { 1, 2, 3, 4 }
};
var output11 = createValues(time, 10, 20, 30, 40);
var output12 = createValues(time, 100, 200, 300, 400);
var output13 = createValues(time, 1000, 2000, 3000, 4000);
var output21 = createValues(time, 50, 60, 70, 80);
var output22 = createValues(time, 500, 600, 700, 800);
var output23 = createValues(time, 5000, 6000, 7000, 8000);
A.CallTo(() => populationSimulation.NumberOfItems).Returns(3);
A.CallTo(() => populationSimulation.AllCovariateValuesFor(CoreConstants.Covariates.GENDER)).Returns(new List <string> {
"Male", "Female", "Male"
});
A.CallTo(() => populationSimulation.AllOutputValuesFor(outputField1.QuantityPath)).Returns(new List <QuantityValues> {
output11, output12, output13
});
A.CallTo(() => populationSimulation.AllOutputValuesFor(outputField2.QuantityPath)).Returns(new List <QuantityValues> {
output21, output22, output23
});
A.CallTo(() => populationSimulation.AllSimulationNames).Returns(new List <string> {
"Sim", "Sim", "Sim"
});
if (observedDataCollection == null)
{
observedDataCollection = new ObservedDataCollection();
}
return(pivotResultCreator.Create(analysis, populationSimulation, observedDataCollection, AggregationFunctions.QuantityAggregation));
}
private void mapCovariateField(PopulationAnalysisField snapshot, PopulationAnalysisCovariateField field)
{
snapshot.Covariate = field.Covariate;
snapshot.GroupingItems = field.GroupingItems.ToArray();
}
private void mapCovariateFieldToModel(PopulationAnalysisField snapshot, PopulationAnalysisCovariateField field)
{
field.Covariate = snapshot.Covariate;
snapshot.GroupingItems?.Each(field.AddGroupingItem);
}
private void drawDistributionFor(PopulationAnalysisCovariateField covariateField)
{
_populationAnalysisFieldDistributionPresenter.Plot(_populationDataCollector, covariateField);
}
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()
{
_newCovariateField = await sut.MapToModel(_snapshot, new SnapshotContext()) as PopulationAnalysisCovariateField;
}
protected override void Because()
{
_covariate = sut.CreateFor(_covariateName, _populationDataCollector);
}
protected override void Because()
{
_populationAnalysisCovariateField = new PopulationAnalysisCovariateField();
_selectedParametersPresenter.CovariateFieldSelected += Raise.With(new CovariateFieldSelectedEventArgs(_covariate, _populationAnalysisCovariateField));
}