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()
{
_cloneManager = A.Fake <ICloneManagerForModel>();
_simulationFactory = A.Fake <ICoreSimulationFactory>();
_parameterIdentificationRun = A.Fake <IParameterIdentificationRun>();
_coreUserSettings = A.Fake <ICoreUserSettings>();
_descriptionCreator = A.Fake <ICategorialParameterIdentificationDescriptionCreator>();
_container = A.Fake <Utility.Container.IContainer>();
A.CallTo(() => _container.Resolve <ICoreSimulationFactory>()).Returns(_simulationFactory);
_coreUserSettings.MaximumNumberOfCoresToUse = 1;
sut = new CategorialParameterIdentificationRunInitializer(_cloneManager, _parameterIdentificationRun, _container, _descriptionCreator, _coreUserSettings);
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.Configuration.RunMode = new CategorialParameterIdentificationRunMode();
_simulation = A.Fake <ISimulation>();
_clonedSimulation = A.Fake <ISimulation>();
A.CallTo(() => _simulationFactory.CreateWithCalculationMethodsFrom(_simulation, A <IEnumerable <CalculationMethodWithCompoundName> > ._)).Returns(_clonedSimulation);
A.CallTo(() => _cloneManager.Clone(_parameterIdentification)).ReturnsLazily(() =>
{
var pi = new ParameterIdentification();
pi.AddSimulation(_simulation);
var identificationParameter = new IdentificationParameter();
identificationParameter.AddLinkedParameter(new ParameterSelection(_simulation, A.Fake <QuantitySelection>()));
pi.AddIdentificationParameter(identificationParameter);
pi.AddOutputMapping(new OutputMapping
{
OutputSelection = new SimulationQuantitySelection(_simulation, A.Fake <QuantitySelection>())
});
pi.Configuration.RunMode = new CategorialParameterIdentificationRunMode();
return(pi);
});
}
protected override void Context()
{
_view = A.Fake <IParameterIdentificationSimulationSelectionView>();
_treeNodeFactory = A.Fake <ITreeNodeFactory>();
_applicationController = A.Fake <IApplicationController>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
_treeNodeContextMenuFactory = A.Fake <ITreeNodeContextMenuFactory>();
_multipleTreeNodeContextMenuFactory = A.Fake <IMultipleTreeNodeContextMenuFactory>();
_dialogCreator = A.Fake <IDialogCreator>();
_parameterIdentificationTask = A.Fake <IParameterIdentificationTask>();
sut = new ParameterIdentificationSimulationSelectionPresenter(_view, _treeNodeFactory, _applicationController, _lazyLoadTask, _treeNodeContextMenuFactory,
_multipleTreeNodeContextMenuFactory, _dialogCreator, _parameterIdentificationTask);
_parameterIdentification = new ParameterIdentification();
_simulation = A.Fake <ISimulation>().WithId("Id").WithName("S");
_parameterIdentification.AddSimulation(_simulation);
_outputMapping = new OutputMapping
{
OutputSelection = new SimulationQuantitySelection(_simulation, new QuantitySelection("PATH", QuantityType.Drug))
};
_parameterIdentification.AddOutputMapping(_outputMapping);
_simulationNode = A.Fake <ITreeNode>();
A.CallTo(() => _treeNodeFactory.CreateFor(_simulation)).Returns(_simulationNode);
_simulationSelectionPresenter = A.Fake <ISelectionSimulationPresenter>();
A.CallTo(() => _applicationController.Start <ISelectionSimulationPresenter>()).Returns(_simulationSelectionPresenter);
sut.EditParameterIdentification(_parameterIdentification);
}
public void AddOutputMapping()
{
var newOutputMapping = new OutputMapping();
_parameterIdentification.AddOutputMapping(newOutputMapping);
_allOutputMappingDTOs.Add(mapFrom(newOutputMapping));
OnStatusChanged();
}
protected override void Context()
{
base.Context();
_parameterIdentification = new ParameterIdentification();
var outputMapping = A.Fake <OutputMapping>();
_parameterIdentification.AddOutputMapping(outputMapping);
_parameterIdentification.AddIdentificationParameter(DomainHelperForSpecs.IdentificationParameter(min: 10, max: 20, startValue: 30));
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("XX");
}
protected override void Context()
{
base.Context();
_parameterIdentification = new ParameterIdentification();
var outputMapping = A.Fake <OutputMapping>();
ConfigureOutputMapping(outputMapping);
_parameterIdentification.AddOutputMapping(outputMapping);
_parameterIdentification.AddIdentificationParameter(DomainHelperForSpecs.IdentificationParameter());
}
protected override void Context()
{
base.Context();
_parameterIdentification = new ParameterIdentification();
var outputMapping = A.Fake <OutputMapping>();
ConfigureOutputMapping(outputMapping);
_parameterIdentification.AddOutputMapping(outputMapping);
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("XX");
}
protected override void Context()
{
base.Context();
_project = A.Fake <IProject>();
_parameterIdentification = new ParameterIdentification();
A.CallTo(() => _executionContext.Project).Returns(_project);
A.CallTo(() => _project.AllParameterIdentifications).Returns(new List <ParameterIdentification> {
_parameterIdentification
});
_simulation = A.Fake <ISimulation>();
_sensitivityAnalysis = new SensitivityAnalysis {
Simulation = _simulation, IsLoaded = true
};
_sensitivityAnalysis.AddSensitivityParameter(new SensitivityParameter());
A.CallTo(() => _project.AllSensitivityAnalyses).Returns(new List <SensitivityAnalysis> {
_sensitivityAnalysis
});
_secondSimulation = A.Fake <ISimulation>();
_parameterIdentification.AddSimulation(_simulation);
_parameterIdentification.AddSimulation(_secondSimulation);
_outputMapping = new OutputMapping {
OutputSelection = new ParameterSelection(_simulation, "a|path")
};
_secondOutputMapping = new OutputMapping {
OutputSelection = new ParameterSelection(_secondSimulation, "a|path")
};
_identificationParameter = new IdentificationParameter();
_linkedParameter = new ParameterSelection(_simulation, "a|path");
_secondLinkedParameter = new ParameterSelection(_secondSimulation, "a|path");
_identificationParameter.AddLinkedParameter(_linkedParameter);
_identificationParameter.AddLinkedParameter(_secondLinkedParameter);
_parameterIdentification.AddIdentificationParameter(_identificationParameter);
_parameterIdentification.AddOutputMapping(_outputMapping);
_parameterIdentification.AddOutputMapping(_secondOutputMapping);
_parameterIdentification.IsLoaded = true;
}
protected override void Context()
{
base.Context();
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.AddIdentificationParameter(DomainHelperForSpecs.IdentificationParameter());
var outputMapping = A.Fake <OutputMapping>();
ConfigureOutputMapping(outputMapping);
_parameterIdentification.AddOutputMapping(outputMapping);
outputMapping.Scaling = Scalings.Log;
var outputMapping2 = A.Fake <OutputMapping>();
ConfigureOutputMapping(outputMapping2);
_parameterIdentification.AddOutputMapping(outputMapping2);
outputMapping2.Scaling = Scalings.Linear;
A.CallTo(() => outputMapping2.Output).Returns(outputMapping.Output);
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("XX");
}
protected override void Context()
{
base.Context();
_sourceParameterIdentification = new ParameterIdentification();
_identificationParameter = new IdentificationParameter();
_cloneOfIdentificationParameter = new IdentificationParameter();
_sourceParameterIdentification.AddSimulation(_simulation);
_sourceParameterIdentification.AddOutputMapping(_outputMapping);
_sourceParameterIdentification.AddIdentificationParameter(_identificationParameter);
_cloneManager = A.Fake <ICloneManager>();
A.CallTo(() => _cloneManager.Clone(_identificationParameter)).Returns(_cloneOfIdentificationParameter);
}
protected override void Context()
{
base.Context();
_parameterIdentification = new ParameterIdentification();
var outputMapping = A.Fake <OutputMapping>();
ConfigureOutputMapping(outputMapping);
_parameterIdentification.AddOutputMapping(outputMapping);
_parameterIdentification.AddIdentificationParameter(DomainHelperForSpecs.IdentificationParameter());
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("XX");
outputMapping.Output.Dimension = DomainHelperForSpecs.FractionDimensionForSpecs();
}
protected override void Context()
{
base.Context();
_dataRepository = A.Fake <DataRepository>();
_parameterIdentification = new ParameterIdentification();
_parameterIdentifications = new List <ParameterIdentification> {
_parameterIdentification, new ParameterIdentification()
};
A.CallTo(() => _executionContext.Project.AllParameterIdentifications).Returns(_parameterIdentifications);
_parameterIdentification.AddOutputMapping(new OutputMapping {
WeightedObservedData = new WeightedObservedData(_dataRepository)
});
}
protected override void Context()
{
base.Context();
_parameterIdentification = new ParameterIdentification();
var outputMapping = A.Fake <OutputMapping>();
ConfigureOutputMapping(outputMapping);
outputMapping.WeightedObservedData = null;
A.CallTo(() => outputMapping.IsValid).Returns(true);
_parameterIdentification.AddOutputMapping(outputMapping);
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("XX");
_parameterIdentification.AddIdentificationParameter(DomainHelperForSpecs.IdentificationParameter());
}
private void addOutputMapping(IQuantity output, string outputPath, DataRepository observedData, ISimulation simulation, ParameterIdentification parameterIdentification)
{
if (parameterIdentification.UsesObservedData(observedData))
{
return;
}
parameterIdentification.AddOutputMapping(new OutputMapping
{
OutputSelection = new SimulationQuantitySelection(simulation, new QuantitySelection(outputPath, output.QuantityType)),
WeightedObservedData = new WeightedObservedData(observedData),
Scaling = DefaultScalingFor(output)
});
}
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()
{
base.Context();
_simulation = new IndividualSimulation();
_usedObservedData = new UsedObservedData {
Id = "dataRepositoryId", Simulation = _simulation
};
_dataRepository = new DataRepository(_usedObservedData.Id);
_simulation.AddUsedObservedData(_usedObservedData);
_parameterIdentification = new ParameterIdentification();
_project.AddObservedData(_dataRepository);
_project.AddParameterIdentification(_parameterIdentification);
var outputMapping = A.Fake <OutputMapping>();
A.CallTo(() => outputMapping.UsesObservedData(_dataRepository)).Returns(true);
A.CallTo(() => outputMapping.UsesSimulation(_simulation)).Returns(false);
_parameterIdentification.AddOutputMapping(outputMapping);
}
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();
_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()
{
_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);
}