protected override void Context()
{
_view = A.Fake <IEditTimeProfileAnalysisChartView>();
_timeProfilerChartPresenter = A.Fake <ITimeProfileChartPresenter>();
_timeProfileChartDataCreator = A.Fake <ITimeProfileChartDataCreator>();
_populationSimulationAnalysisStarter = A.Fake <IPopulationSimulationAnalysisStarter>();
_populationAnalysisTask = A.Fake <IPopulationAnalysisTask>();
_colorGenerator = A.Fake <IColorGenerator>();
_observedDataTask = A.Fake <IObservedDataTask>();
_pkAnalysisPresenter = A.Fake <IPopulationPKAnalysisPresenter>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_presenterSettingsTask = A.Fake <IPresentationSettingsTask>();
sut = new EditTimeProfileAnalysisChartPresenter(_view, _timeProfilerChartPresenter, _timeProfileChartDataCreator,
_populationSimulationAnalysisStarter, _populationAnalysisTask, _colorGenerator, _observedDataTask, _pkAnalysisPresenter, _dimensionRepository, _presenterSettingsTask);
_timeProfileAnalysisChart = new TimeProfileAnalysisChart();
_populationStatisticalAnalysis = new PopulationStatisticalAnalysis();
_timeProfileAnalysisChart.PopulationAnalysis = _populationStatisticalAnalysis;
_populationDataCollector = A.Fake <IPopulationDataCollector>();
sut.InitializeAnalysis(_timeProfileAnalysisChart, _populationDataCollector);
_observedDataRepository = DomainHelperForSpecs.ObservedData();
var data = new DragDropInfo(
new List <ITreeNode> {
new ObservedDataNode(new ClassifiableObservedData {
Subject = _observedDataRepository
})
}
);
_dragEventArgs = new DragEventArgs(new DataObject(data), 0, 0, 0, DragDropEffects.All, DragDropEffects.All);
_chartData = new ChartData <TimeProfileXValue, TimeProfileYValue>(null, null);
var concentrationDimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
var yAxis = new AxisData(concentrationDimension, concentrationDimension.DefaultUnit, Scalings.Linear);
_paneData = new PaneData <TimeProfileXValue, TimeProfileYValue>(yAxis);
_chartData.AddPane(_paneData);
A.CallTo(_timeProfileChartDataCreator).WithReturnType <ChartData <TimeProfileXValue, TimeProfileYValue> >().Returns(_chartData);
var outputField = new PopulationAnalysisOutputField {
Dimension = DomainHelperForSpecs.MassConcentrationDimensionForSpecs()
};
_populationStatisticalAnalysis.Add(outputField);
A.CallTo(() => _dimensionRepository.MergedDimensionFor(A <NumericFieldContext> ._)).Returns(concentrationDimension);
}
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 mapOutputFieldToModel(PopulationAnalysisField snapshot, PopulationAnalysisOutputField field)
{
mapQuantityFieldToModel(snapshot, field);
field.Color = ModelValueFor(snapshot.Color, field.Color);
}
private void mapOutputFieldToSnapshot(PopulationAnalysisField snapshot, PopulationAnalysisOutputField field)
{
mapQuantityFieldToSnapshot(snapshot, field);
snapshot.Color = field.Color;
}
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()
{
_newOutputField = await sut.MapToModel(_snapshot, new SnapshotContext()) as PopulationAnalysisOutputField;
}
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);
}
