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()
{
_populationRunner = A.Fake <IPopulationRunner>();
_exceptionManager = A.Fake <IExceptionManager>();
_eventPubliser = A.Fake <IEventPublisher>();
_progressUpdater = A.Fake <IProgressUpdater>();
_progressManager = A.Fake <IProgressManager>();
_simulationResultsSynchronizer = A.Fake <ISimulationResultsSynchronizer>();
_simMapper = A.Fake <ISimulationToModelCoreSimulationMapper>();
_popExportTask = A.Fake <IPopulationExportTask>();
_simulationPersistableUpdater = A.Fake <ISimulationPersistableUpdater>();
_userSettings = A.Fake <ICoreUserSettings>();
_populationSimulationAnalysisSynchronizer = A.Fake <IPopulationSimulationAnalysisSynchronizer>();
sut = new PopulationSimulationEngine(_populationRunner,
_progressManager,
_eventPubliser,
_exceptionManager,
_simulationResultsSynchronizer,
_popExportTask,
_simMapper,
_simulationPersistableUpdater,
_userSettings,
_populationSimulationAnalysisSynchronizer);
A.CallTo(() => _progressManager.Create()).Returns(_progressUpdater);
}
public DistributionDataCreator(IBinIntervalsCreator binIntervalsCreator, IRepresentationInfoRepository representationInfoRepository, IEntityPathResolver entityPathResolver, ICoreUserSettings userSettings)
{
_binIntervalsCreator = binIntervalsCreator;
_representationInfoRepository = representationInfoRepository;
_entityPathResolver = entityPathResolver;
_userSettings = userSettings;
}
public PopulationRepository(IFlatPopulationRepository flatPopultionRepository, IFlatPopulationToPopulationMapper flatPopMapper,
IRepresentationInfoRepository representationInfoRepository, ICoreUserSettings userSettings)
{
_flatPopultionRepository = flatPopultionRepository;
_flatPopMapper = flatPopMapper;
_representationInfoRepository = representationInfoRepository;
_userSettings = userSettings;
}
public ParameterAlternativeFactory(IObjectBaseFactory objectBaseFactory, ICloner cloner,
ISpeciesRepository speciesRepository, ICoreUserSettings userSettings)
{
_objectBaseFactory = objectBaseFactory;
_cloner = cloner;
_speciesRepository = speciesRepository;
_userSettings = userSettings;
}
protected override void Context()
{
_dialogCreator = A.Fake <IDialogCreator>();
_userSettings = A.Fake <ICoreUserSettings>();
_configuration = A.Fake <IPKSimConfiguration>();
sut = new TemplateDatabaseCreator(_dialogCreator, _userSettings, _configuration);
}
public SpeciesRepository(IFlatSpeciesRepository flatSpeciesRepository, IFlatSpeciesToSpeciesMapper flatSpeciesMapper,
ICoreUserSettings userSettings, IRepresentationInfoRepository representationInfoRepository)
{
_flatSpeciesRepository = flatSpeciesRepository;
_flatSpeciesMapper = flatSpeciesMapper;
_userSettings = userSettings;
_representationInfoRepository = representationInfoRepository;
}
protected override void Context()
{
_eventPublisher = A.Fake <IEventPublisher>();
_parameterIdentificationRunFactory = A.Fake <IParameterIdentificationRunFactory>();
_parameterIdentification = new ParameterIdentification().WithId("PI");
_coreUserSettings = A.Fake <ICoreUserSettings>();
A.CallTo(() => _coreUserSettings.MaximumNumberOfCoresToUse).Returns(2);
sut = new ParameterIdentificationEngine(_eventPublisher, _parameterIdentificationRunFactory, _coreUserSettings);
}
public SimulationSettingsRetriever(IApplicationController applicationController, IProjectRetriever projectRetriever,
IEntityPathResolver entityPathResolver, IKeyPathMapper keyPathMapper, ICoreUserSettings userSettings)
{
_applicationController = applicationController;
_projectRetriever = projectRetriever;
_entityPathResolver = entityPathResolver;
_keyPathMapper = keyPathMapper;
_userSettings = userSettings;
}
public SimulationAnalysisCreator(IPopulationSimulationAnalysisStarter populationSimulationAnalysisStarter,
IExecutionContext executionContext, IContainerTask containerTask, IPKSimChartFactory chartFactory,
ICoreUserSettings userSettings, ICloner cloner) : base(containerTask, executionContext)
{
_populationSimulationAnalysisStarter = populationSimulationAnalysisStarter;
_chartFactory = chartFactory;
_userSettings = userSettings;
_cloner = cloner;
}
protected override void Context()
{
_populationSimulationSettingsPresenter = A.Fake <IPopulationSimulationSettingsPresenter>();
_applicationController = A.Fake <IApplicationController>();
_projectRetriever = A.Fake <IPKSimProjectRetriever>();
_simulationPersistableUpdater = A.Fake <ISimulationPersistableUpdater>();
_project = A.Fake <PKSimProject>();
_compound1 = A.Fake <Compound>();
_individual = A.Fake <Individual>();
_human = new Species().WithName(CoreConstants.Species.HUMAN);
_rat = new Species().WithName(CoreConstants.Species.RAT);
_mouse = new Species().WithName(CoreConstants.Species.MOUSE);
A.CallTo(() => _individual.Species).Returns(_human);
_populationSimulation = A.Fake <PopulationSimulation>();
A.CallTo(() => _populationSimulation.Compounds).Returns(new[] { _compound1 });
A.CallTo(() => _populationSimulation.Individual).Returns(_individual);
_keyPathMapper = A.Fake <IKeyPathMapper>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_userSettings = A.Fake <ICoreUserSettings>();
_originalSettings = new OutputSelections();
A.CallTo(() => _populationSimulation.OutputSelections).Returns(_originalSettings);
_populationSimulation.Model = new Model();
_populationSimulation.Model.Root = new Container();
_compound1.Name = "DRUG";
var organism = new Organism();
var peripheralVenousBlood = new Container().WithName(CoreConstants.Organ.PeripheralVenousBlood);
var venousBlood = new Container().WithName(CoreConstants.Organ.VenousBlood);
var venousBloodPlasma = new Container().WithName(CoreConstants.Compartment.Plasma).WithParentContainer(venousBlood);
var drugPeripheralBlood = new Container().WithName(_compound1.Name);
var drugVenousBlood = new Container().WithName(_compound1.Name);
var periperhalVenousBloodObserver = new Observer {
Name = CoreConstants.Observer.PLASMA_PERIPHERAL_VENOUS_BLOOD
};
drugPeripheralBlood.Add(periperhalVenousBloodObserver);
var venousBloodObserver = new Observer {
Name = CoreConstants.Observer.CONCENTRATION
};
drugVenousBlood.Add(venousBloodObserver);
peripheralVenousBlood.Add(drugPeripheralBlood);
venousBloodPlasma.Add(drugVenousBlood);
organism.Add(peripheralVenousBlood);
organism.Add(venousBlood);
_populationSimulation.Model.Root.Add(organism);
A.CallTo(() => _projectRetriever.Current).Returns(_project);
A.CallTo(() => _applicationController.Start <ISimulationOutputSelectionPresenter <PopulationSimulation> >()).Returns(_populationSimulationSettingsPresenter);
sut = new SimulationSettingsRetriever(_applicationController, _projectRetriever, _entityPathResolver, _keyPathMapper, _userSettings, _simulationPersistableUpdater);
A.CallTo(() => _entityPathResolver.PathFor(periperhalVenousBloodObserver)).Returns("PERIPHERAL_OBSERVER");
A.CallTo(() => _entityPathResolver.PathFor(venousBloodObserver)).Returns("VENOUS_BLOOD_OBSERVER");
}
public ParameterIdentificationEngine(
IEventPublisher eventPublisher,
IParameterIdentificationRunFactory parameterIdentificationRunFactory,
ICoreUserSettings coreUserSettings)
{
_eventPublisher = eventPublisher;
_parameterIdentificationRunFactory = parameterIdentificationRunFactory;
_coreUserSettings = coreUserSettings;
_cancellationTokenSource = new CancellationTokenSource();
}
public TemplateTaskQuery(ITemplateDatabase templateDatabase, IStringSerializer stringSerializer,
IObjectIdResetter objectIdResetter, IPKSimConfiguration pkSimConfiguration, ICoreUserSettings userSettings, ITemplateDatabaseConverter templateDatabaseConverter)
{
_objectIdResetter = objectIdResetter;
_pkSimConfiguration = pkSimConfiguration;
_userSettings = userSettings;
_templateDatabaseConverter = templateDatabaseConverter;
_templateDatabase = templateDatabase;
_stringSerializer = stringSerializer;
}
protected override void Context()
{
_userSettings = A.Fake <ICoreUserSettings>();
_userSettings.NumberOfBins = 2;
_userSettings.NumberOfIndividualsPerBin = 100;
_representationInfoRep = A.Fake <IRepresentationInfoRepository>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_binIntervalCreator = new BinIntervalsCreator(_userSettings);
sut = new DistributionDataCreator(_binIntervalCreator, _representationInfoRep, _entityPathResolver, _userSettings);
}
protected override void Context()
{
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_cloner = A.Fake <ICloner>();
_speciesRepository = A.Fake <ISpeciesRepository>();
//necessary to create compound since default parameter willl be added to the group based on compound parameters
_compound = new Compound();
_compoundParameterGroup = new ParameterAlternativeGroup();
_compound.AddParameterAlternativeGroup(_compoundParameterGroup);
_userSettings = A.Fake <ICoreUserSettings>();
sut = new ParameterAlternativeFactory(_objectBaseFactory, _cloner, _speciesRepository, _userSettings);
}
protected override void Context()
{
_populationSimulationAnalysisStarter = A.Fake <IPopulationSimulationAnalysisStarter>();
_executionContext = A.Fake <IExecutionContext>();
_containerTask = A.Fake <IContainerTask>();
_chartFactory = A.Fake <IPKSimChartFactory>();
_userSettings = A.Fake <ICoreUserSettings>();
_cloner = A.Fake <ICloner>();
sut = new SimulationAnalysisCreator(_populationSimulationAnalysisStarter, _executionContext,
_containerTask, _chartFactory, _userSettings, _cloner);
}
public CategorialParameterIdentificationRunInitializer(
ICloneManagerForModel cloneManager,
IParameterIdentificationRun parameterIdentificationRun,
Utility.Container.IContainer container,
ICategorialParameterIdentificationDescriptionCreator descriptionCreator,
ICoreUserSettings coreUserSettings) : base(cloneManager,
parameterIdentificationRun)
{
_container = container;
_descriptionCreator = descriptionCreator;
_coreUserSettings = coreUserSettings;
}
protected SimulationOutputSelectionPresenter(TView view, IQuantitySelectionPresenter quantitySelectionPresenter,
ISimulationPersistableUpdater simulationPersistableUpdater, IPKSimProjectRetriever projectRetriever, IDialogCreator dialogCreator, ICoreUserSettings userSettings)
: base(view)
{
_quantitySelectionPresenter = quantitySelectionPresenter;
_simulationPersistableUpdater = simulationPersistableUpdater;
_projectRetriever = projectRetriever;
_dialogCreator = dialogCreator;
_userSettings = userSettings;
_quantitySelectionPresenter.StatusChanged += quantitySelectionChanged;
_view.AddSettingsView(_quantitySelectionPresenter.BaseView);
_quantitySelectionPresenter.ExpandAllGroups = false;
}
public SensitivityAnalysisEngine(IEventPublisher eventPublisher, ISensitivyAnalysisVariationDataCreator sensitivyAnalysisVariationDataCreator,
IPopulationRunner populationRunner, ICoreUserSettings userSettings, ISimulationToModelCoreSimulationMapper modelCoreSimulationMapper,
ISensitivityAnalysisRunResultCalculator runResultCalculator, ISimulationPersistableUpdater simulationPersistableUpdater)
{
_eventPublisher = eventPublisher;
_sensitivyAnalysisVariationDataCreator = sensitivyAnalysisVariationDataCreator;
_populationRunner = populationRunner;
_userSettings = userSettings;
_modelCoreSimulationMapper = modelCoreSimulationMapper;
_runResultCalculator = runResultCalculator;
_simulationPersistableUpdater = simulationPersistableUpdater;
_populationRunner.Terminated += terminated;
_populationRunner.SimulationProgress += simulationProgress;
}
public SensitivityAnalysisRunner(
ISensitivityAnalysisEngineFactory sensitivityAnalysisEngineFactory,
IDialogCreator dialogCreator,
IEntityValidationTask entityValidationTask,
IOSPSuiteExecutionContext executionContext,
ICoreUserSettings coreUserSettings
)
{
_sensitivityAnalysisEngineFactory = sensitivityAnalysisEngineFactory;
_dialogCreator = dialogCreator;
_entityValidationTask = entityValidationTask;
_executionContext = executionContext;
_coreUserSettings = coreUserSettings;
}
public ParameterIdentificationRun(IResidualCalculatorFactory residualCalculatorFactory, ITimeGridUpdater timeGridUpdater,
ISimModelBatchFactory simModelBatchFactory, ISimulationToModelCoreSimulationMapper modelCoreSimulationMapper,
IParameterIdentificationAlgorithmToOptmizationAlgorithmMapper optimizationAlgorithmMapper, IOutputSelectionUpdater outputSelectionUpdater,
ICoreUserSettings coreUserSettings, IJacobianMatrixCalculator jacobianMatrixCalculator)
{
_residualCalculatorFactory = residualCalculatorFactory;
_timeGridUpdater = timeGridUpdater;
_simModelBatchFactory = simModelBatchFactory;
_modelCoreSimulationMapper = modelCoreSimulationMapper;
_optimizationAlgorithmMapper = optimizationAlgorithmMapper;
_outputSelectionUpdater = outputSelectionUpdater;
_coreUserSettings = coreUserSettings;
_jacobianMatrixCalculator = jacobianMatrixCalculator;
}
public SimulationSettingsRetriever(
IApplicationController applicationController,
IPKSimProjectRetriever projectRetriever,
IEntityPathResolver entityPathResolver,
IKeyPathMapper keyPathMapper,
ICoreUserSettings userSettings,
ISimulationPersistableUpdater simulationPersistableUpdater)
{
_applicationController = applicationController;
_projectRetriever = projectRetriever;
_entityPathResolver = entityPathResolver;
_keyPathMapper = keyPathMapper;
_userSettings = userSettings;
_simulationPersistableUpdater = simulationPersistableUpdater;
}
protected override void Context()
{
_eventPublisher = A.Fake <IEventPublisher>();
_sensitivyAnalysisVariationDataCreator = A.Fake <ISensitivyAnalysisVariationDataCreator>();
_populationRunner = A.Fake <IPopulationRunner>();
_userSettings = A.Fake <ICoreUserSettings>();
_modelCoreSimulationMapper = A.Fake <ISimulationToModelCoreSimulationMapper>();
_runResultCalculator = A.Fake <ISensitivityAnalysisRunResultCalculator>();
_simulationPersistableUpdater = A.Fake <ISimulationPersistableUpdater>();
sut = new SensitivityAnalysisEngine(_eventPublisher, _sensitivyAnalysisVariationDataCreator, _populationRunner, _userSettings, _modelCoreSimulationMapper, _runResultCalculator, _simulationPersistableUpdater);
_sensitivityAnalysis = A.Fake <SensitivityAnalysis>();
_modelCoreSimulation = A.Fake <IModelCoreSimulation>();
A.CallTo(() => _modelCoreSimulationMapper.MapFrom(_sensitivityAnalysis.Simulation, true)).Returns(_modelCoreSimulation);
}
public PopulationSimulationEngine(IPopulationRunner populationRunner, IProgressManager progressManager,
IEventPublisher eventPublisher, IExceptionManager exceptionManager,
ISimulationResultsSynchronizer simulationResultsSynchronizer, IPopulationExportTask populationExporter,
ISimulationToModelCoreSimulationMapper modelCoreSimulationMapper, ISimulationPersistableUpdater simulationPersistableUpdater, ICoreUserSettings userSettings,
IPopulationSimulationAnalysisSynchronizer populationSimulationAnalysisSynchronizer)
{
_populationRunner = populationRunner;
_progressManager = progressManager;
_eventPublisher = eventPublisher;
_exceptionManager = exceptionManager;
_simulationResultsSynchronizer = simulationResultsSynchronizer;
_populationExporter = populationExporter;
_modelCoreSimulationMapper = modelCoreSimulationMapper;
_simulationPersistableUpdater = simulationPersistableUpdater;
_userSettings = userSettings;
_populationSimulationAnalysisSynchronizer = populationSimulationAnalysisSynchronizer;
_populationRunner.Terminated += terminated;
_populationRunner.SimulationProgress += simulationProgress;
}
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 BinIntervalsCreator(ICoreUserSettings userSettings)
{
_userSettings = userSettings;
}
public SolverSettingsFactory(OSPSuite.Core.Domain.ISolverSettingsFactory solverSettingsFactory, ICoreUserSettings userSettings)
{
_solverSettingsFactory = solverSettingsFactory;
_userSettings = userSettings;
}
protected override void Because()
{
_result = sut.Load();
}
protected override void Context()
{
_userSettings = A.Fake <ICoreUserSettings>();
_allValues = new List <double>();
sut = new BinIntervalsCreator(_userSettings);
}
public TemplateDatabaseCreator(IDialogCreator dialogCreator, ICoreUserSettings userSettings, IPKSimConfiguration configuration)
{
_dialogCreator = dialogCreator;
_userSettings = userSettings;
_configuration = configuration;
}
