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);
}
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;
}
public void AddSimulationTo(ParameterIdentification parameterIdentification, ISimulation simulation)
{
if (parameterIdentification.UsesSimulation(simulation))
{
return;
}
_executionContext.Load(simulation);
parameterIdentification.AddSimulation(simulation);
addOutputMappingsFor(simulation, parameterIdentification);
}
protected override void Context()
{
_journalTask = A.Fake <IJournalTask>();
_activeSubjectRetriever = A.Fake <IActiveSubjectRetriever>();
_observedDataRepository = A.Fake <IObservedDataRepository>();
_executionContext = A.Fake <IOSPSuiteExecutionContext>();
sut = new AddParameterAnalysableToActiveJournalPageUICommand(_journalTask, _observedDataRepository, _executionContext, _activeSubjectRetriever);
_parameterIdentification = new ParameterIdentification();
sut.Subject = _parameterIdentification;
_simulation1 = A.Fake <ISimulation>();
_simulation2 = A.Fake <ISimulation>();
_parameterIdentification.AddSimulation(_simulation1);
_parameterIdentification.AddSimulation(_simulation2);
_obs1 = new DataRepository("OBS1");
_obs2 = new DataRepository("OBS2");
A.CallTo(() => _observedDataRepository.AllObservedDataUsedBy(_parameterIdentification)).Returns(new[] { _obs1, _obs2 });
}
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()
{
_view = A.Fake <IParameterIdentificationDataSelectionView>();
_simulationSelectionPresenter = A.Fake <IParameterIdentificationSimulationSelectionPresenter>();
_outputMappingPresenter = A.Fake <IParameterIdentificationOutputMappingPresenter>();
_weightedObservedDataCollectorPresenter = A.Fake <IParameterIdentificationWeightedObservedDataCollectorPresenter>();
sut = new ParameterIdentificationDataSelectionPresenter(_view, _simulationSelectionPresenter, _outputMappingPresenter, _weightedObservedDataCollectorPresenter);
_simulation = A.Fake <ISimulation>().WithId("Sim");
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.AddSimulation(_simulation);
sut.EditParameterIdentification(_parameterIdentification);
}
protected override void Context()
{
base.Context();
_project = A.Fake <IProject>();
_parameterIdentification = A.Fake <ParameterIdentification>();
_context = A.Fake <IMoBiContext>();
_simulationReferenceUpdater = A.Fake <ISimulationReferenceUpdater>();
_simulationParameterOriginIdUpdater = A.Fake <ISimulationParameterOriginIdUpdater>();
A.CallTo(() => _context.PublishEvent(A <SimulationUnloadEvent> ._))
.Invokes(x => _event = x.GetArgument <SimulationUnloadEvent>(0));
A.CallTo(() => _context.Project).Returns(_project);
A.CallTo(() => _context.Resolve <ISimulationReferenceUpdater>()).Returns(_simulationReferenceUpdater);
A.CallTo(() => _context.Resolve <ISimulationParameterOriginIdUpdater>()).Returns(_simulationParameterOriginIdUpdater);
A.CallTo(() => _project.AllParameterIdentifications).Returns(new[] { _parameterIdentification });
_parameterIdentification.AddSimulation(_simulation);
}
protected override void Context()
{
_entitiesInSimulationRetriever = A.Fake <IEntitiesInSimulationRetriever>();
_view = A.Fake <ISimulationParametersView>();
_simulationParameterSelectionDTOMapper = A.Fake <IQuantityToSimulationParameterSelectionDTOMapper>();
_groupRepository = A.Fake <IGroupRepository>();
_parameterSelector = A.Fake <IParameterAnalysableParameterSelector>();
sut = new SimulationParametersPresenter(_view, _entitiesInSimulationRetriever, _simulationParameterSelectionDTOMapper, _groupRepository, _parameterSelector);
_allParameters = new PathCacheForSpecs <IParameter>();
_parameterIdentification = new ParameterIdentification();
_simulation = A.Fake <ISimulation>();
_parameterIdentification.AddSimulation(_simulation);
A.CallTo(() => _entitiesInSimulationRetriever.ParametersFrom(_simulation, A <Func <IParameter, bool> > ._)).Returns(_allParameters);
A.CallTo(() => _view.BindTo(A <IEnumerable <SimulationParameterSelectionDTO> > ._))
.Invokes(x => _allQuantitySelectionDTO = x.GetArgument <IEnumerable <SimulationParameterSelectionDTO> >(0));
}
protected override void Context()
{
_view = A.Fake <IEditParameterIdentificationView>();
_subPresenterItemManager = SubPresenterHelper.Create <IParameterIdentificationItemPresenter>();
_parameterIdentificationDataSelectionPresenter = _subPresenterItemManager.CreateFake(ParameterIdentificationItems.Data);
_parameterIdentificationParameterSelectionPresenter = _subPresenterItemManager.CreateFake(ParameterIdentificationItems.Parameters);
_parameterIdentificationConfigurationPresenter = _subPresenterItemManager.CreateFake(ParameterIdentificationItems.Configuration);
_simulationAnalysisPresenterFactory = A.Fake <ISimulationAnalysisPresenterFactory>();
_contextMenuFactory = A.Fake <ISimulationAnalysisPresenterContextMenuFactory>();
_presentationSettingsTask = A.Fake <IPresentationSettingsTask>();
_simulationAnalysisCreator = A.Fake <IParameterIdentificationAnalysisCreator>();
_executionContext = A.Fake <IOSPSuiteExecutionContext>();
_simulation = A.Fake <ISimulation>();
sut = new EditParameterIdentificationPresenter(_view, _subPresenterItemManager, _executionContext, _simulationAnalysisPresenterFactory, _contextMenuFactory, _presentationSettingsTask, _simulationAnalysisCreator);
sut.InitializeWith(A.Fake <ICommandCollector>());
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.AddSimulation(_simulation);
}
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()
{
_containerTask = A.Fake <IContainerTask>();
_identificationParameterTask = A.Fake <IIdentificationParameterTask>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
sut = new IdentificationParameterFactory(_objectBaseFactory, _containerTask, _identificationParameterTask);
_simulationParameterSelection = new List <ParameterSelection>();
_parameterIdentification = new ParameterIdentification();
_simulation = A.Fake <ISimulation>();
_simulation.Model.Root = new Container();
A.CallTo(() => _objectBaseFactory.Create <IdentificationParameter>()).Returns(new IdentificationParameter());
_parameterIdentification.AddSimulation(_simulation);
_lengthLiver = A.Fake <IParameter>().WithName("Length").WithDimension(DomainHelperForSpecs.LengthDimensionForSpecs());
_fractionLiver = A.Fake <IParameter>().WithName("Fraction").WithDimension(DomainHelperForSpecs.FractionDimensionForSpecs());
_lengthKidney = A.Fake <IParameter>().WithName("Length").WithDimension(DomainHelperForSpecs.LengthDimensionForSpecs());
var logDimension = A.Fake <IDimension>();
A.CallTo(() => logDimension.Name).Returns(Constants.Dimension.LOG_UNITS);
_lipoKidney = A.Fake <IParameter>().WithName("Lipo").WithDimension(logDimension);
_fracKidney = A.Fake <IParameter>().WithName("Frac").WithDimension(DomainHelperForSpecs.FractionDimensionForSpecs());
var liver = new Container().WithName("Liver");
var kidney = new Container().WithName("Kidney");
liver.Add(_lengthLiver);
liver.Add(_fractionLiver);
kidney.Add(_lengthKidney);
kidney.Add(_lipoKidney);
kidney.Add(_fracKidney);
_simulation.Model.Root.Add(liver);
_simulation.Model.Root.Add(kidney);
_simulationParameterSelection.Add(new ParameterSelection(_simulation, new QuantitySelection("Liver|Length", QuantityType.Parameter)));
}
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);
}
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);
}
public void should_not_add_the_simulation_twice()
{
A.CallTo(() => _parameterIdentification.AddSimulation(_simulation)).MustNotHaveHappened();
}