protected override void Context()
{
base.Context();
_dataRepository = DomainHelperForSpecs.ObservedData(
"TOTO",
_dimensionTask.DimensionByName(Constants.Dimension.TIME),
_dimensionTask.DimensionByName(Constants.Dimension.MOLAR_CONCENTRATION),
"OBS_COL"
);
_obsColumn = _dataRepository.Columns.FindByName("OBS_COL");
}
protected override void Context()
{
base.Context();
A.CallTo(() => _dataRepositoryTask.ExportToCsvAsync(A <IEnumerable <DataColumn> > ._, _fileName, A <DataColumnExportOptions> ._))
.Invokes(x => _exportOptions = x.GetArgument <DataColumnExportOptions>(2));
_dataColumn = DomainHelperForSpecs.ObservedData().FirstDataColumn();
_dataColumn.Name = "TOTO";
A.CallTo(() => _quantityDisplayPathMapper.DisplayPathAsStringFor(_simulation, _dataColumn, false)).Returns("NEW NAME");
}
protected override void Context()
{
_observedData = DomainHelperForSpecs.ObservedData("TOTO");
_outputMapping = new OutputMapping {
WeightedObservedData = new WeightedObservedData(_observedData)
{
Id = 5
}
};
_outputMappingDTO = new OutputMappingDTO(_outputMapping);
sut = new WeightedObservedDataFormatter(_outputMappingDTO);
}
protected override void Context()
{
base.Context();
sut = new ResidualCalculatorForOnlyObservedData(_timeGridRestrictor, _dimensionFactory);
_outputMapping.Scaling = Scalings.Linear;
_outputMapping2 = A.Fake <OutputMapping>();
A.CallTo(() => _outputMapping2.FullOutputPath).Returns(_fullOutputPath);
_observedData2 = DomainHelperForSpecs.ObservedData().WithName("OBS2");
_outputMapping2.WeightedObservedData = new WeightedObservedData(_observedData2);
_outputMappings.Add(_outputMapping2);
}
protected override void Context()
{
base.Context();
_dataRepository = DomainHelperForSpecs.ObservedData();
_sim1 = new IndividualSimulation {
Name = "Sim1"
};
_sim2 = new IndividualSimulation {
Name = "Sim2"
};
_sim1.AddUsedObservedData(_dataRepository);
A.CallTo(() => _project.AllUsersOfObservedData).Returns(new [] { _sim1, _sim2, });
}
protected override void Context()
{
base.Context();
_dataRepository = DomainHelperForSpecs.ObservedData();
_sim1 = new IndividualSimulation {
Name = "Sim1"
};
_sim2 = new IndividualSimulation {
Name = "Sim2"
};
_sim1.AddUsedObservedData(_dataRepository);
_project.AddBuildingBlock(_sim1);
_project.AddBuildingBlock(_sim2);
}
protected override void Context()
{
_presentationSettingsTask = A.Fake <IPresentationSettingsTask>();
_view = A.Fake <IParameterIdentificationMultipleRunsAnalysisView>();
_chartEditorAndDisplayPresenter = A.Fake <IChartEditorAndDisplayPresenter>();
_curveNamer = A.Fake <ICurveNamer>();
_pathElementsMapper = A.Fake <IDataColumnToPathElementsMapper>();
_chartTemplatingTask = A.Fake <IChartTemplatingTask>();
_dimensionFactory = A.Fake <IDimensionFactory>();
_displayUnitRetriever = A.Fake <IDisplayUnitRetriever>();
_chartEditorLayoutTask = A.Fake <IChartEditorLayoutTask>();
_projectRetreiver = A.Fake <IProjectRetriever>();
_chartPresenterContext = A.Fake <ChartPresenterContext>();
A.CallTo(() => _chartPresenterContext.EditorAndDisplayPresenter).Returns(_chartEditorAndDisplayPresenter);
A.CallTo(() => _chartPresenterContext.CurveNamer).Returns(_curveNamer);
A.CallTo(() => _chartPresenterContext.DataColumnToPathElementsMapper).Returns(_pathElementsMapper);
A.CallTo(() => _chartPresenterContext.TemplatingTask).Returns(_chartTemplatingTask);
A.CallTo(() => _chartPresenterContext.PresenterSettingsTask).Returns(_presentationSettingsTask);
A.CallTo(() => _chartPresenterContext.DimensionFactory).Returns(_dimensionFactory);
A.CallTo(() => _chartPresenterContext.EditorLayoutTask).Returns(_chartEditorLayoutTask);
A.CallTo(() => _chartPresenterContext.ProjectRetriever).Returns(_projectRetreiver);
sut = new ParameterIdentificationTimeProfileChartPresenter(_view, _chartPresenterContext, _displayUnitRetriever);
_timeProfileAnalysis = new ParameterIdentificationTimeProfileChart();
_outputMapping1 = A.Fake <OutputMapping>();
_outputMapping2 = A.Fake <OutputMapping>();
_observedData1 = DomainHelperForSpecs.ObservedData();
_observedData2 = DomainHelperForSpecs.ObservedData();
A.CallTo(() => _outputMapping1.WeightedObservedData).Returns(new WeightedObservedData(_observedData1));
A.CallTo(() => _outputMapping2.WeightedObservedData).Returns(new WeightedObservedData(_observedData2));
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.AddOutputMapping(_outputMapping1);
_parameterIdentification.AddOutputMapping(_outputMapping2);
_parameterIdentificationRunResult = A.Fake <ParameterIdentificationRunResult>();
_parameterIdentification.AddResult(_parameterIdentificationRunResult);
_optimizationRunResult = new OptimizationRunResult();
_parameterIdentificationRunResult.BestResult = _optimizationRunResult;
_parameterIdentificationRunResult = A.Fake <ParameterIdentificationRunResult>();
_parameterIdentification.AddResult(_parameterIdentificationRunResult);
_optimizationRunResult2 = new OptimizationRunResult();
_parameterIdentificationRunResult.BestResult = _optimizationRunResult2;
}
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);
}
protected override void Context()
{
_dialogCreator = A.Fake <IDialogCreator>();
_context = A.Fake <IOSPSuiteExecutionContext>();
_dataRepositoryTask = A.Fake <IDataRepositoryExportTask>();
_containerTask = A.Fake <IContainerTask>();
_objectTypeResolver = A.Fake <IObjectTypeResolver>();
sut = new ObservedDataTaskForSpecs(_dialogCreator, _context, _dataRepositoryTask, _containerTask, _objectTypeResolver);
_obsData1 = DomainHelperForSpecs.ObservedData("OBS1");
_obsData2 = DomainHelperForSpecs.ObservedData("OBS2");
A.CallTo(() => _context.Project.AllUsersOfObservedData).Returns(_allUserOfObservedData);
}
protected override async Task Context()
{
await base.Context();
_runOptions.Validate = true;
_expectedOutputPath = Path.Combine(_qualificationConfiguration.OutputFolder, PROJECT_NAME);
_expectedObsDataPath = _qualificationConfiguration.ObservedDataFolder;
DirectoryHelper.DirectoryExists = s => string.Equals(s, _expectedOutputPath);
DirectoryHelper.DeleteDirectory = (s, b) => _deletedDirectory = s;
_observedData = DomainHelperForSpecs.ObservedData().WithName("OBS");
_project.AddObservedData(_observedData);
}
protected override void Context()
{
base.Context();
_solubilityDataRepository = DomainHelperForSpecs.ObservedData("SolubilityTable");
A.CallTo(() => _formulaFactory.CreateTableFormula(A <bool> ._)).Returns(new TableFormula {
UseDerivedValues = true
});
A.CallTo(() => _dataImporter.ImportDataSets(
A <IReadOnlyList <MetaDataCategory> > .Ignored,
A <IReadOnlyList <ColumnInfo> > .Ignored,
A <DataImporterSettings> .Ignored,
A <string> .Ignored)).Returns((new List <DataRepository>()
{
_solubilityDataRepository
}, null));
}
protected override void Context()
{
_eventPublisher = A.Fake <IEventPublisher>();
_view = A.Fake <IParameterIdentificationWeightedObservedDataCollectorView>();
_applicationController = A.Fake <IApplicationController>();
sut = new ParameterIdentificationWeightedObservedDataCollectorPresenter(_view, _applicationController, _eventPublisher);
_parameterIdentification = new ParameterIdentification();
_weightedObservedData = new WeightedObservedData(DomainHelperForSpecs.ObservedData());
_outputMapping = new OutputMapping {
WeightedObservedData = _weightedObservedData
};
_parameterIdentification.AddOutputMapping(_outputMapping);
_presenter = A.Fake <IParameterIdentificationWeightedObservedDataPresenter>();
A.CallTo(() => _applicationController.Start <IParameterIdentificationWeightedObservedDataPresenter>()).Returns(_presenter);
}
protected override void Context()
{
_view = A.Fake <IParameterIdentificationSingleRunAnalysisView>();
_chartEditorAndDisplayPresenter = A.Fake <IChartEditorAndDisplayPresenter>();
_curveNamer = A.Fake <ICurveNamer>();
_dataColumnToPathElementsMapper = A.Fake <IDataColumnToPathElementsMapper>();
_chartTemplatingTask = A.Fake <IChartTemplatingTask>();
_presentationSettingsTask = A.Fake <IPresentationSettingsTask>();
_dimensionFactory = A.Fake <IDimensionFactory>();
_predictedVsObservedService = A.Fake <IPredictedVsObservedChartService>();
_chartEditorLayoutTask = A.Fake <IChartEditorLayoutTask>();
_projectRetreiver = A.Fake <IProjectRetriever>();
_chartPresenterContext = A.Fake <ChartPresenterContext>();
A.CallTo(() => _chartPresenterContext.EditorAndDisplayPresenter).Returns(_chartEditorAndDisplayPresenter);
A.CallTo(() => _chartPresenterContext.CurveNamer).Returns(_curveNamer);
A.CallTo(() => _chartPresenterContext.DataColumnToPathElementsMapper).Returns(_dataColumnToPathElementsMapper);
A.CallTo(() => _chartPresenterContext.TemplatingTask).Returns(_chartTemplatingTask);
A.CallTo(() => _chartPresenterContext.PresenterSettingsTask).Returns(_presentationSettingsTask);
A.CallTo(() => _chartPresenterContext.DimensionFactory).Returns(_dimensionFactory);
A.CallTo(() => _chartPresenterContext.EditorLayoutTask).Returns(_chartEditorLayoutTask);
A.CallTo(() => _chartPresenterContext.ProjectRetriever).Returns(_projectRetreiver);
_observationData = DomainHelperForSpecs.ObservedData();
_simulationData = DomainHelperForSpecs.IndividualSimulationDataRepositoryFor("Simulation");
_noDimensionColumnForSimulation = _simulationData.FirstDataColumn();
_predictedVsObservedChart = new ParameterIdentificationPredictedVsObservedChart().WithAxes();
_parameterIdentification = A.Fake <ParameterIdentification>();
sut = new ParameterIdentificationPredictedVsObservedChartPresenter(_view, _chartPresenterContext, _predictedVsObservedService);
_parameterIdentificationRunResult = A.Fake <ParameterIdentificationRunResult>();
A.CallTo(() => _parameterIdentification.Results).Returns(new[] { _parameterIdentificationRunResult });
_residualResults = new ResidualsResult();
_optimizationRunResult = new OptimizationRunResult {
ResidualsResult = _residualResults, SimulationResults = new List <DataRepository> {
_simulationData
}
};
_parameterIdentificationRunResult.BestResult = _optimizationRunResult;
sut.InitializeAnalysis(_predictedVsObservedChart);
}
protected override void Context()
{
_view = A.Fake <IDataBrowserView>();
sut = new DataBrowserPresenter(_view);
sut.SetDisplayQuantityPathDefinition(x => new PathElements {
{ PathElement.Name, new PathElementDTO {
DisplayName = x.Name
} }
});
A.CallTo(() => _view.BindTo(A <IEnumerable <DataColumnDTO> > ._))
.Invokes(x => _allDataColumnDTOs = x.GetArgument <IEnumerable <DataColumnDTO> >(0).ToList());
_obsData1 = DomainHelperForSpecs.ObservedData("OBS1");
_column1 = _obsData1.FirstDataColumn();
_obsData2 = DomainHelperForSpecs.ObservedData("OBS2");
_column2 = _obsData2.FirstDataColumn();
}
protected override void Context()
{
base.Context();
_bestColumn = DomainHelperForSpecs.ObservedData().FirstDataColumn();
_currentColumn = DomainHelperForSpecs.ObservedData().FirstDataColumn();
_bestResult = A.Fake <OptimizationRunResult>();
_currentResult = A.Fake <OptimizationRunResult>();
sut.EditParameterIdentification(_parameterIdentification);
sut.SelectedOutput = A.Fake <OutputMapping>();
A.CallTo(() => _bestResult.SimulationResultFor(A <string> ._)).Returns(_bestColumn);
A.CallTo(() => _currentResult.SimulationResultFor(A <string> ._)).Returns(_currentColumn);
_runState = A.Fake <ParameterIdentificationRunState>();
A.CallTo(() => _runState.BestResult).Returns(_bestResult);
A.CallTo(() => _runState.CurrentResult).Returns(_currentResult);
}
protected override async Task Context()
{
await base.Context();
_expectedOutputPath = Path.Combine(_qualificationConfiguration.OutputFolder, PROJECT_NAME);
DirectoryHelper.DirectoryExists = s => string.Equals(s, _expectedOutputPath);
DirectoryHelper.DeleteDirectory = (s, b) => _deletedDirectory = s;
_simulationName = "S1";
_simulation = new Simulation {
Name = _simulationName
};
_individualSimulation = new IndividualSimulation {
Name = _simulationName
};
_input = new Input {
Project = PROJECT_NAME, Name = _simulationName, SectionId = 2, Type = PKSimBuildingBlockType.Simulation, SectionLevel = 5
};
_expectedSimulationPath = Path.Combine(_expectedOutputPath, _simulationName);
_simulationExport = new SimulationMapping {
Project = PROJECT_NAME, Simulation = _simulationName, Path = _expectedSimulationPath
};
_simulationExports = new[] { _simulationExport };
A.CallTo(() => _exportSimulationRunner.ExportSimulationsIn(_project, A <ExportRunOptions> ._))
.Invokes(x => _exportOptions = x.GetArgument <ExportRunOptions>(1))
.Returns(_simulationExports);
_observedData = DomainHelperForSpecs.ObservedData().WithName("OBS");
_project.AddObservedData(_observedData);
_projectSnapshot.Simulations = new[] { _simulation };
_expectedObservedDataXlsFullPath = Path.Combine(_qualificationConfiguration.ObservedDataFolder, $"{_observedData.Name}{Constants.Filter.XLSX_EXTENSION}");
_expectedObservedDataCsvFullPath = Path.Combine(_qualificationConfiguration.ObservedDataFolder, $"{_observedData.Name}{Constants.Filter.CSV_EXTENSION}");
_expectedInputFullPath = Path.Combine(_qualificationConfiguration.InputsFolder, PROJECT_NAME, PKSimBuildingBlockType.Simulation.ToString(), $"{_simulationName}{CoreConstants.Filter.MARKDOWN_EXTENSION}");
A.CallTo(() => _jsonSerializer.Serialize(A <QualificationMapping> ._, _qualificationConfiguration.MappingFile))
.Invokes(x => _mapping = x.GetArgument <QualificationMapping>(0));
_project.AddBuildingBlock(_individualSimulation);
_qualificationConfiguration.Inputs = new[] { _input };
_qualificationConfiguration.Simulations = new[] { _simulationName, };
_runOptions.Run = true;
}
protected override void Context()
{
base.Context();
_outputPath = "Liver|Cell|Drug";
_simulation = A.Fake <ISimulation>().WithId("Sim");
_parameterIdentification = new ParameterIdentification();
_output1 = A.Fake <IQuantity>();
var allOutputs = new PathCacheForSpecs <IQuantity> {
{ _outputPath, _output1 }
};
A.CallTo(() => _entitiesInSimulationRetriever.OutputsFrom(_simulation)).Returns(allOutputs);
_observedData1 = DomainHelperForSpecs.ObservedData("OBS1");
_observedData2 = DomainHelperForSpecs.ObservedData("OBS2");
_observedData3 = DomainHelperForSpecs.ObservedData("OBS3");
A.CallTo(() => _observedDataRepository.AllObservedDataUsedBy(_simulation)).Returns(new[] { _observedData1, _observedData2 });
var simulationQuantitySelection = A.Fake <SimulationQuantitySelection>();
A.CallTo(() => simulationQuantitySelection.Path).Returns(_outputPath);
_parameterIdentification.AddOutputMapping(new OutputMapping {
WeightedObservedData = new WeightedObservedData(_observedData2), OutputSelection = simulationQuantitySelection
});
_observedData1.ExtendedProperties.Add(new ExtendedProperty <string> {
Name = ObservedData.MOLECULE, Value = "Drug"
});
_observedData1.ExtendedProperties.Add(new ExtendedProperty <string> {
Name = ObservedData.ORGAN, Value = "Liver"
});
_observedData1.ExtendedProperties.Add(new ExtendedProperty <string> {
Name = ObservedData.COMPARTMENT, Value = "Cell"
});
_observedData3.ExtendedProperties.Add(new ExtendedProperty <string> {
Name = ObservedData.ORGAN, Value = "Kidney"
});
}
protected override void Context()
{
base.Context();
var otherSimulationDataColumn = new DataColumn("Col", DomainHelperForSpecs.ConcentrationDimensionForSpecs(), _simulationDataColumn.BaseGrid)
{
Values = new[] { 0f, 2.5f, 0.9f, 0.9f, 0.5f },
DataInfo = { Origin = ColumnOrigins.Calculation },
QuantityInfo = new QuantityInfo("Concentration", new[] { "Sim", "Organism", "Liver", "Plasma", "Concentration" }, QuantityType.Drug)
};
_simulationResults.Add(otherSimulationDataColumn);
_outputMapping2 = A.Fake <OutputMapping>();
A.CallTo(() => _outputMapping2.FullOutputPath).Returns(otherSimulationDataColumn.PathAsString);
var observedData2 = DomainHelperForSpecs.ObservedData().WithName("OBS2");
_outputMapping2.WeightedObservedData = new WeightedObservedData(observedData2);
_outputMappings.Add(_outputMapping2);
sut = new ResidualCalculatorForOnlyObservedData(_timeGridRestrictor, _dimensionFactory);
}
protected override void Context()
{
base.Context();
_simulation = A.Fake <ISimulation>();
_project = A.Fake <IProject>();
_parameterIdentification = new ParameterIdentification();
A.CallTo(() => _executionContext.Project).Returns(_project);
A.CallTo(() => _project.AllParameterIdentifications).Returns(new[] { _parameterIdentification });
_parameterIdentification.AddSimulation(_simulation);
_initialObjectPath = new ObjectPath("oldName", "path");
var parameterIdentificationRunResult = new ParameterIdentificationRunResult {
BestResult = new OptimizationRunResult()
};
_simulationDataRepository = DomainHelperForSpecs.SimulationDataRepositoryFor("oldName");
_observationDataRepository = DomainHelperForSpecs.ObservedData();
_observationDataRepository.AllButBaseGrid().Each(x => x.QuantityInfo.Path = _initialObjectPath);
_simulationDataRepository.AllButBaseGrid().Each(x => x.QuantityInfo.Path = _initialObjectPath);
parameterIdentificationRunResult.BestResult.AddResult(_simulationDataRepository);
_residualsResult = new ResidualsResult();
_residualsResult.AddOutputResiduals(_initialObjectPath.PathAsString, _observationDataRepository, new List <Residual> {
new Residual(0, 1, 1)
});
parameterIdentificationRunResult.BestResult.ResidualsResult = _residualsResult;
_parameterIdentification.AddResult(parameterIdentificationRunResult);
var outputMapping = new OutputMapping
{
WeightedObservedData = new WeightedObservedData(_observationDataRepository),
OutputSelection = new ParameterSelection(_simulation, _initialObjectPath.PathAsString)
};
_parameterIdentification.AddOutputMapping(outputMapping);
}
protected override void Context()
{
_identification = A.Fake <ParameterIdentification>();
_dimensionFactory = A.Fake <IDimensionFactory>();
_displayUnitRetriever = A.Fake <IDisplayUnitRetriever>();
A.CallTo(_dimensionFactory).WithReturnType <IDimension>().ReturnsLazily(x => x.Arguments.Get <IWithDimension>(0).Dimension);
_predictedVsObservedChart = new ParameterIdentificationPredictedVsObservedChart().WithAxes();
_observedConcentrationData = DomainHelperForSpecs.ObservedData();
_concentrationObservationColumn = _observedConcentrationData.FirstDataColumn();
_simulationData = DomainHelperForSpecs.IndividualSimulationDataRepositoryFor("Simulation");
_simulationColumn = _simulationData.FirstDataColumn();
_fractionObservedData = DomainHelperForSpecs.ObservedData();
_fractionObservationColumn = _fractionObservedData.FirstDataColumn();
_fractionObservationColumn.Dimension = DomainHelperForSpecs.NoDimension();
sut = new PredictedVsObservedChartService(_dimensionFactory, _displayUnitRetriever);
}
protected override void Context()
{
_dimensionFactory = A.Fake <IDimensionFactory>();
sut = new CurveChart().WithAxes();
_xAxis = sut.AxisBy(AxisTypes.X);
_yAxis = sut.AxisBy(AxisTypes.Y);
_obsData1 = DomainHelperForSpecs.ObservedData();
_obsData2 = DomainHelperForSpecs.ObservedData();
_curveOnYAxis = new Curve {
yAxisType = AxisTypes.Y
};
_curveOnYAxis.SetxData(_obsData1.BaseGrid, _dimensionFactory);
_curveOnYAxis.SetyData(_obsData1.FirstDataColumn(), _dimensionFactory);
_curveOnY2Axis = new Curve {
yAxisType = AxisTypes.Y2
};
_curveOnY2Axis.SetxData(_obsData2.BaseGrid, _dimensionFactory);
_curveOnY2Axis.SetyData(_obsData2.FirstDataColumn(), _dimensionFactory);
}
protected override void Context()
{
base.Context();
_dimensionFactory = A.Fake <IDimensionFactory>();
_individualSimulationComparison = new IndividualSimulationComparison();
var dataRepository = DomainHelperForSpecs.ObservedData();
var curve = new Curve();
curve.SetxData(dataRepository.BaseGrid, _dimensionFactory);
curve.SetyData(dataRepository.FirstDataColumn(), _dimensionFactory);
_individualSimulationComparison.AddCurve(curve);
sut.InitializeAnalysis(_individualSimulationComparison);
_simulation = A.Fake <IndividualSimulation>();
A.CallTo(() => _simulation.HasResults).Returns(true);
var simulationNode = new SimulationNode(new ClassifiableSimulation {
Subject = _simulation
});
_dropEventArgs = new DragEventArgs(new DataObject(new DragDropInfo(new List <SimulationNode> {
simulationNode
})), 0, 0, 0, DragDropEffects.All, DragDropEffects.All);
}
protected override void Context()
{
_binIntervalCreator = A.Fake <IBinIntervalsCreator>();
_observedData = DomainHelperForSpecs.ObservedData();
sut = new ResidualDistibutionDataCreator(_binIntervalCreator);
}
protected override void Context()
{
base.Context();
_dataRepository = DomainHelperForSpecs.ObservedData();
}
public override void GlobalContext()
{
base.GlobalContext();
_observedData = DomainHelperForSpecs.ObservedData();
_sim1 = new IndividualSimulation
{
Id = "Sim1",
Name = "Sim1",
IsLoaded = true,
Model = new Model {
Root = new Container()
}
};
_sim1.Model.Root.Add(new Container {
new Parameter().WithName("P")
}.WithName("Liver"));
_sim2 = new IndividualSimulation
{
Id = "Sim2",
Name = "Sim2",
IsLoaded = true,
Model = new Model {
Root = new Container()
}
};
_sim2.Model.Root.Add(new Container {
new Parameter().WithName("P")
}.WithName("Liver"));
_objectBaseRepository = IoC.Resolve <IWithIdRepository>();
var workspace = IoC.Resolve <ICoreWorkspace>();
_project = IoC.Resolve <PKSimProject>();
workspace.Project = _project;
_objectBaseRepository.Register(_sim1);
_objectBaseRepository.Register(_sim2);
_project.AddObservedData(_observedData);
_project.AddBuildingBlock(_sim1);
_project.AddBuildingBlock(_sim2);
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.AddSimulation(_sim1);
_parameterIdentification.AddSimulation(_sim2);
_outputMapping = new OutputMapping
{
WeightedObservedData = new WeightedObservedData(_observedData),
OutputSelection = new SimulationQuantitySelection(_sim1, new QuantitySelection("A|B", QuantityType.Metabolite)),
Weight = 5,
Scaling = Scalings.Log
};
_outputMapping.WeightedObservedData.Weights[1] = 10;
_parameterIdentification.AddOutputMapping(_outputMapping);
_identificationParameter = DomainHelperForSpecs.IdentificationParameter(min: 1, max: 10, startValue: 5);
_parameterSelection1 = new ParameterSelection(_sim1, new QuantitySelection("Liver|P", QuantityType.Parameter));
_parameterSelection2 = new ParameterSelection(_sim2, new QuantitySelection("Liver|P", QuantityType.Parameter));
_identificationParameter.AddLinkedParameter(_parameterSelection1);
_identificationParameter.AddLinkedParameter(_parameterSelection2);
_parameterIdentification.AddIdentificationParameter(_identificationParameter);
_identificationParameter.Scaling = Scalings.Linear;
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("AA");
_parameterIdentification.AlgorithmProperties.Add(new ExtendedProperty <double> {
Name = "Toto", Value = 5
});
_runResult = new ParameterIdentificationRunResult();
_parameterIdentification.AddResult(_runResult);
_parameterIdentification.AddAnalysis(new ParameterIdentificationPredictedVsObservedChart());
_parameterIdentification.AddAnalysis(new ParameterIdentificationTimeProfileChart());
_parameterIdentification.AddAnalysis(new ParameterIdentificationResidualHistogram());
_parameterIdentification.AddAnalysis(new ParameterIdentificationResidualVsTimeChart());
GlobalBecause();
}
protected override void Context()
{
base.Context();
_dataRepository = DomainHelperForSpecs.ObservedData();
_dataRepository.FirstDataColumn().Dimension = DomainHelperForSpecs.FractionDimensionForSpecs();
}
protected override void Context()
{
base.Context();
_dataRepository = DomainHelperForSpecs.ObservedData();
A.CallTo(() => _mdiChildPresenter.Subject).Returns(_dataRepository);
}
protected override void Context()
{
_observedData = DomainHelperForSpecs.ObservedData();
sut = new WeightedObservedData(_observedData);
}
protected override void Context()
{
_modelCoreSimulationMapper = A.Fake <ISimulationToModelCoreSimulationMapper>();
_residualCalculatorFactory = A.Fake <IResidualCalculatorFactory>();
_timeGridUpdater = A.Fake <ITimeGridUpdater>();
_simModelBatchFactory = A.Fake <ISimModelBatchFactory>();
_optimizationAlgorithmMapper = A.Fake <IParameterIdentificationAlgorithmToOptmizationAlgorithmMapper>();
_outputSelectionUpdater = A.Fake <IOutputSelectionUpdater>();
_coreUserSettings = A.Fake <ICoreUserSettings>();
_jacobianMatrixCalculator = A.Fake <IJacobianMatrixCalculator>();
_coreUserSettings.MaximumNumberOfCoresToUse = 2;
sut = new ParameterIdentificationRun(_residualCalculatorFactory, _timeGridUpdater, _simModelBatchFactory, _modelCoreSimulationMapper,
_optimizationAlgorithmMapper, _outputSelectionUpdater, _coreUserSettings, _jacobianMatrixCalculator);
_simulation = A.Fake <ISimulation>();
_parameter1 = A.Fake <IParameter>();
_parameter1.Dimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
_parameter1.Value = 15;
_parameter2 = A.Fake <IParameter>();
_parameter2.Value = 35;
_parameter2.Dimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.Configuration.LLOQMode = LLOQModes.OnlyObservedData;
_parameterIdentification.Configuration.RemoveLLOQMode = RemoveLLOQModes.NoTrailing;
_parameterIdentification.AddSimulation(_simulation);
_parameterSelection1 = ParameterSelectionFor(_parameter1, "ParameterPath1");
_parameterSelection2 = ParameterSelectionFor(_parameter2, "ParameterPath2");
_identificationParameter = DomainHelperForSpecs.IdentificationParameter("IdParam", min: 10, max: 20, startValue: 15);
_identificationParameter.AddLinkedParameter(_parameterSelection1);
_identificationParameter.AddLinkedParameter(_parameterSelection2);
_modelCoreSimulation = A.Fake <IModelCoreSimulation>();
A.CallTo(() => _modelCoreSimulationMapper.MapFrom(_simulation, true)).Returns(_modelCoreSimulation);
_outputMapping = A.Fake <OutputMapping>();
A.CallTo(() => _outputMapping.UsesSimulation(_simulation)).Returns(true);
A.CallTo(() => _outputMapping.WeightedObservedData.ObservedData).Returns(DomainHelperForSpecs.ObservedData());
_parameterIdentification.AddOutputMapping(_outputMapping);
_simModelBatch = A.Fake <ISimModelBatch>();
A.CallTo(() => _simModelBatchFactory.Create()).Returns(_simModelBatch);
_parameterIdentification.AddIdentificationParameter(_identificationParameter);
_residualCalculator = A.Fake <IResidualCalculator>();
A.CallTo(_residualCalculatorFactory).WithReturnType <IResidualCalculator>().Returns(_residualCalculator);
_algorithm = A.Fake <IOptimizationAlgorithm>();
A.CallTo(() => _optimizationAlgorithmMapper.MapFrom(_parameterIdentification.AlgorithmProperties)).Returns(_algorithm);
_cancellationTokenSource = new CancellationTokenSource();
_cancellationToken = _cancellationTokenSource.Token;
_runInitializer = A.Fake <IParameterIdentifcationRunInitializer>();
A.CallTo(() => _runInitializer.InitializeRun()).ReturnsAsync(_parameterIdentification);
PerformExtraInitializationSteps();
sut.InitializeWith(_runInitializer);
}
protected override void Context()
{
_view = A.Fake <IParameterIdentificationOutputMappingView>();
_observedDataRepository = A.Fake <IObservedDataRepository>();
_entitiesInSimulationRetriever = A.Fake <IEntitiesInSimulationRetriever>();
_outputMappingDTOMapper = A.Fake <IOutputMappingToOutputMappingDTOMapper>();
_simulationQuantitySelectionDTOMapper = A.Fake <IQuantityToSimulationQuantitySelectionDTOMapper>();
_parameterIdentificationTask = A.Fake <IParameterIdentificationTask>();
sut = new ParameterIdentificationOutputMappingPresenter(_view, _entitiesInSimulationRetriever, _observedDataRepository, _outputMappingDTOMapper,
_simulationQuantitySelectionDTOMapper, _parameterIdentificationTask);
_observedData1 = DomainHelperForSpecs.ObservedData("Obs1").WithName("Obs1");
_weightedObservedData1 = new WeightedObservedData(_observedData1);
_observedData2 = DomainHelperForSpecs.ObservedData("Obs2").WithName("Obs2");
_weightedObservedData2 = new WeightedObservedData(_observedData2);
_parameterIdentification = new ParameterIdentification();
_simulation1 = A.Fake <ISimulation>().WithId("Id1");
_simulation2 = A.Fake <ISimulation>().WithId("Id2");
_usedObservedData1 = new UsedObservedData {
Id = "Obs1"
};
_usedObservedData2 = new UsedObservedData {
Id = "Obs2"
};
A.CallTo(() => _observedDataRepository.All()).Returns(new[] { _observedData1, _observedData2 });
A.CallTo(() => _observedDataRepository.AllObservedDataUsedBy(_simulation1)).Returns(new[] { _observedData2 });
A.CallTo(() => _observedDataRepository.AllObservedDataUsedBy(_simulation2)).Returns(new[] { _observedData1, _observedData2 });
_parameterIdentification.AddSimulation(_simulation1);
_parameterIdentification.AddSimulation(_simulation2);
_quantity1 = A.Fake <IQuantity>();
_quantity2 = A.Fake <IQuantity>();
_output1 = A.Fake <SimulationQuantitySelectionDTO>();
A.CallTo(() => _output1.Simulation).Returns(_simulation1);
_output2 = A.Fake <SimulationQuantitySelectionDTO>();
A.CallTo(() => _output2.Simulation).Returns(_simulation2);
A.CallTo(() => _entitiesInSimulationRetriever.OutputsFrom(_simulation1)).Returns(new PathCache <IQuantity>(new EntityPathResolverForSpecs())
{
{ "AA", _quantity1 }
});
A.CallTo(() => _entitiesInSimulationRetriever.OutputsFrom(_simulation2)).Returns(new PathCache <IQuantity>(new EntityPathResolverForSpecs())
{
{ "BB", _quantity2 }
});
A.CallTo(() => _simulationQuantitySelectionDTOMapper.MapFrom(_simulation1, _quantity1)).Returns(_output1);
A.CallTo(() => _simulationQuantitySelectionDTOMapper.MapFrom(_simulation2, _quantity2)).Returns(_output2);
A.CallTo(() => _view.BindTo(A <IEnumerable <OutputMappingDTO> > ._))
.Invokes(x => _allOutputMappingDTOs = x.GetArgument <IEnumerable <OutputMappingDTO> >(0));
sut.EditParameterIdentification(_parameterIdentification);
_outputMapping1 = A.Fake <OutputMapping>();
_outputMapping2 = A.Fake <OutputMapping>();
_outputMappingDTO1 = new OutputMappingDTO(_outputMapping1)
{
Output = _output1
};
_outputMappingDTO2 = new OutputMappingDTO(_outputMapping2)
{
Output = _output2
};
A.CallTo(() => _outputMapping1.Simulation).Returns(_simulation1);
A.CallTo(() => _outputMapping2.Simulation).Returns(_simulation2);
A.CallTo(() => _outputMappingDTOMapper.MapFrom(_outputMapping1, A <IEnumerable <SimulationQuantitySelectionDTO> > ._)).Returns(_outputMappingDTO1);
A.CallTo(() => _outputMappingDTOMapper.MapFrom(_outputMapping2, A <IEnumerable <SimulationQuantitySelectionDTO> > ._)).Returns(_outputMappingDTO2);
}
