protected override void Context()
{
_view = A.Fake <IAdvancedParametersView>();
_allConstantParameterGroupsPresenter = A.Fake <IPopulationParameterGroupsPresenter>();
_advancedParameterGroupsPresenter = A.Fake <IPopulationParameterGroupsPresenter>();
_advancedParameterPresenter = A.Fake <IAdvancedParameterPresenter>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_advancedParametersTask = A.Fake <IAdvancedParametersTask>();
_eventPublisher = A.Fake <IEventPublisher>();
A.CallTo(() => _allConstantParameterGroupsPresenter.View).Returns(A.Fake <IPopulationParameterGroupsView>());
A.CallTo(() => _advancedParameterGroupsPresenter.View).Returns(A.Fake <IPopulationParameterGroupsView>());
A.CallTo(() => _advancedParameterPresenter.View).Returns(A.Fake <IAdvancedParameterView>());
_population = A.Fake <RandomPopulation>();
_commandRegister = A.Fake <ICommandCollector>();
_allConstantParameters = new List <IParameter>();
_allAdvancedParameters = new List <IParameter>();
_allParameters = new List <IParameter>();
A.CallTo(() => _population.AllIndividualParameters()).Returns(_allParameters);
A.CallTo(() => _population.AllConstantParameters(_entityPathResolver)).Returns(_allConstantParameters);
A.CallTo(() => _population.AllAdvancedParameters(_entityPathResolver)).Returns(_allAdvancedParameters);
_para1 = A.Fake <IParameter>().WithName("_para1");
_para1.Visible = true;
_para1.CanBeVaried = true;
_para1.CanBeVariedInPopulation = true;
_para1.Editable = true;
_para2 = A.Fake <IParameter>().WithName("_para2");
_para2.Editable = true;
_para2.Visible = true;
_para2.CanBeVaried = true;
_para2.CanBeVariedInPopulation = true;
_advancedPara1 = A.Fake <IParameter>().WithName("_advancedPara1");
_advancedPara1.Visible = true;
_advancedPara1.Editable = true;
_advancedPara1.CanBeVaried = true;
_advancedPara1.CanBeVariedInPopulation = true;
_pathPara1 = "_pathPara1";
_pathPara2 = "_pathPara2";
_pathAdvancedPara1 = "_pathAdvancedPara1";
_allParameters.AddRange(new[] { _para1, _para2, _advancedPara1 });
_allConstantParameters.AddRange(new[] { _para1, _para2 });
_allAdvancedParameters.AddRange(new[] { _advancedPara1 });
A.CallTo(() => _entityPathResolver.PathFor(_para1)).Returns(_pathPara1);
A.CallTo(() => _entityPathResolver.PathFor(_para2)).Returns(_pathPara2);
A.CallTo(() => _entityPathResolver.PathFor(_advancedPara1)).Returns(_pathAdvancedPara1);
_representationInfoRepository = A.Fake <IRepresentationInfoRepository>();
sut = new PopulationAdvancedParametersPresenter(_view, _entityPathResolver, _allConstantParameterGroupsPresenter, _advancedParameterGroupsPresenter, _advancedParameterPresenter,
_advancedParametersTask, _eventPublisher);
sut.InitializeWith(_commandRegister);
}
public IndividualFactory(
OriginDataMapper originDataMapper,
ICoreIndividualFactory individualFactory,
IIndividualToIndividualValuesMapper individualValuesMapper,
IOntogenyFactorsRetriever ontogenyFactorsRetriever,
IEntityPathResolver entityPathResolver,
IContainerTask containerTask)
{
_originDataMapper = originDataMapper;
_individualFactory = individualFactory;
_individualValuesMapper = individualValuesMapper;
_ontogenyFactorsRetriever = ontogenyFactorsRetriever;
_entityPathResolver = entityPathResolver;
_containerTask = containerTask;
}
protected override void Context()
{
_modelConstructor = A.Fake <IModelConstructor>();
_buildConfigurationFactory = A.Fake <IBuildConfigurationFactory>();
_objectPathFactory = A.Fake <IObjectPathFactory>();
_context = A.Fake <IMoBiContext>();
_applicationController = A.Fake <IMoBiApplicationController>();
_configurePresenter = A.Fake <IConfigureSimulationPresenter>();
_validationVisitor = A.Fake <IDimensionValidator>();
_affectedBuildingBlockRetriever = A.Fake <IAffectedBuildingBlockRetriever>();
_entityPathResolver = new EntityPathResolverForSpecs();
A.CallTo(() => _applicationController.Start <IConfigureSimulationPresenter>()).Returns(_configurePresenter);
sut = new SimulationUpdateTask(_modelConstructor, _buildConfigurationFactory, _context, _applicationController, _validationVisitor, _entityPathResolver, _affectedBuildingBlockRetriever);
}
public PKSimSpatialStructureFactory(IObjectBaseFactory objectBaseFactory, IParameterContainerTask parameterContainerTask,
IModelContainerQuery modelContainerQuery, IModelNeighborhoodQuery modelNeighborhoodQuery,
IParameterSetUpdater parameterSetUpdater, IParameterIdUpdater parameterIdUpdater,
INeighborhoodFinalizer neighborhoodFinalizer, IEntityPathResolver entityPathResolver) : base(objectBaseFactory)
{
_objectBaseFactory = objectBaseFactory;
_parameterContainerTask = parameterContainerTask;
_modelContainerQuery = modelContainerQuery;
_modelNeighborhoodQuery = modelNeighborhoodQuery;
_parameterSetUpdater = parameterSetUpdater;
_parameterIdUpdater = parameterIdUpdater;
_neighborhoodFinalizer = neighborhoodFinalizer;
_entityPathResolver = entityPathResolver;
}
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()
{
_entityPathResolver = A.Fake <IEntityPathResolver>();
_view = A.Fake <ICompoundTypeGroupView>();
_representationInfoRep = A.Fake <IRepresentationInfoRepository>();
_mapper = A.Fake <ICompoundToCompoundTypeDTOMapper>();
_parameterTask = A.Fake <IParameterTask>();
_editValueOriginPresenter = A.Fake <IEditValueOriginPresenter>();
sut = new CompoundTypeGroupPresenter(_view, _representationInfoRep, _mapper, _parameterTask, _entityPathResolver, _editValueOriginPresenter);
_parameters = new List <IParameter>();
_compoundTypesDTOs = new List <TypePKaDTO>();
A.CallTo(() => _mapper.MapFrom(_parameters)).Returns(_compoundTypesDTOs);
}
public ParameterToParameterDTOMapper(
IRepresentationInfoRepository representationInfoRepository,
IFormulaToFormulaTypeMapper formulaTypeMapper,
IPathToPathElementsMapper parameterDisplayPathMapper,
IFavoriteRepository favoriteRepository,
IEntityPathResolver entityPathResolver,
IParameterListOfValuesRetriever parameterListOfValuesRetriever)
{
_representationInfoRepository = representationInfoRepository;
_formulaTypeMapper = formulaTypeMapper;
_parameterDisplayPathMapper = parameterDisplayPathMapper;
_favoriteRepository = favoriteRepository;
_entityPathResolver = entityPathResolver;
_parameterListOfValuesRetriever = parameterListOfValuesRetriever;
}
protected EditFavoritesPresenter(
IEditFavoritesView view,
IFavoriteRepository favoriteRepository,
IEntityPathResolver entityPathResolver,
IEditParameterListPresenter editParameterListPresenter,
IFavoriteTask favoriteTask)
: base(view)
{
_favoriteRepository = favoriteRepository;
_entityPathResolver = entityPathResolver;
_editParameterListPresenter = editParameterListPresenter;
_favoriteTask = favoriteTask;
_parameterCache = new Cache <string, IParameter>(pathFor, s => null);
AddSubPresenters(_editParameterListPresenter);
_view.AddParametersView(_editParameterListPresenter.BaseView);
}
public FlatContainerToApplicationMapper(IParameterContainerTask parameterContainerTask,
IApplicationTransportRepository applicTransportRepo,
IEntityPathResolver entityPathResolver,
IFlatContainerRepository flatContainerRepo,
IFlatContainerIdToContainerMapper flatContainerIdMapper,
IObjectBaseFactory objectBaseFactory,
IFlatContainerToEventBuilderMapper eventMapper)
{
_parameterContainerTask = parameterContainerTask;
_applicTransportRepo = applicTransportRepo;
_entityPathResolver = entityPathResolver;
_flatContainerRepo = flatContainerRepo;
_flatContainerIdMapper = flatContainerIdMapper;
_objectBaseFactory = objectBaseFactory;
_eventMapper = eventMapper;
}
public PKAnalysesTask(ILazyLoadTask lazyLoadTask,
IPKValuesCalculator pkValuesCalculator,
IPKParameterRepository pkParameterRepository,
IPKCalculationOptionsFactory pkCalculationOptionsFactory,
IEntityPathResolver entityPathResolver,
IPKValuesToPKAnalysisMapper pkMapper,
IDimensionRepository dimensionRepository) : base(lazyLoadTask, pkValuesCalculator, pkParameterRepository, pkCalculationOptionsFactory)
{
_lazyLoadTask = lazyLoadTask;
_entityPathResolver = entityPathResolver;
_pkMapper = pkMapper;
_dimensionRepository = dimensionRepository;
_pkValuesCalculator = pkValuesCalculator;
_pkCalculationOptionsFactory = pkCalculationOptionsFactory;
_pkParameterRepository = pkParameterRepository;
}
public Converter514To521(IParameterValuesCacheConverter parameterValuesCacheConverter, IEntityPathResolver entityPathResolver, ICompoundConverter compoundConverter,
IDefaultIndividualRetriever defaultIndividualRetriever, ICloner cloner, IFormulaAndDimensionConverter formulaAndDimensionConverter,
ICalculationMethodRepository calculationMethodRepository, IDimensionRepository dimensionRepository, ISimulationPersistableUpdater simulationPersistableUpdater,
IIndividualCalculationMethodsUpdater individualCalculationMethodsUpdater)
{
_parameterValuesCacheConverter = parameterValuesCacheConverter;
_entityPathResolver = entityPathResolver;
_compoundConverter = compoundConverter;
_defaultIndividualRetriever = defaultIndividualRetriever;
_cloner = cloner;
_formulaAndDimensionConverter = formulaAndDimensionConverter;
_calculationMethodRepository = calculationMethodRepository;
_dimensionRepository = dimensionRepository;
_simulationPersistableUpdater = simulationPersistableUpdater;
_individualCalculationMethodsUpdater = individualCalculationMethodsUpdater;
}
public PopulationExportTask(IApplicationController applicationController, IEntityPathResolver entityPathResolver,
ILazyLoadTask lazyLoadTask, ISimModelExporter simModelExporter, ISimulationToModelCoreSimulationMapper modelCoreSimulationMapper,
IWorkspace workspace, IPKSimConfiguration configuration, ISimulationSettingsRetriever simulationSettingsRetriever,
IDialogCreator dialogCreator, ICloner cloner)
{
_applicationController = applicationController;
_entityPathResolver = entityPathResolver;
_lazyLoadTask = lazyLoadTask;
_simModelExporter = simModelExporter;
_modelCoreSimulationMapper = modelCoreSimulationMapper;
_workspace = workspace;
_configuration = configuration;
_simulationSettingsRetriever = simulationSettingsRetriever;
_dialogCreator = dialogCreator;
_cloner = cloner;
}
protected override void Context()
{
_parameterStartValueBuildingBlock = new ParameterStartValuesBuildingBlock().WithId("PSVBB");
_objectPath = new ObjectPath("A", "B", "P");
_parameter = A.Fake <IParameter>().WithName("P").WithId("P");
sut = new AddParameterStartValueFromQuantityInSimulationCommand(_parameter, _parameterStartValueBuildingBlock);
_context = A.Fake <IMoBiContext>();
_parameterStartValuesCreator = A.Fake <IParameterStartValuesCreator>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
A.CallTo(() => _context.Resolve <IEntityPathResolver>()).Returns(_entityPathResolver);
A.CallTo(() => _context.Resolve <IParameterStartValuesCreator>()).Returns(_parameterStartValuesCreator);
A.CallTo(() => _context.Get <IParameter>(_parameter.Id)).Returns(_parameter);
A.CallTo(() => _context.Get <IStartValuesBuildingBlock <IParameterStartValue> >(_parameterStartValueBuildingBlock.Id)).Returns(_parameterStartValueBuildingBlock);
A.CallTo(() => _entityPathResolver.ObjectPathFor(_parameter, false)).Returns(_objectPath);
}
public SimulationMapper(
SolverSettingsMapper solverSettingsMapper,
OutputSchemaMapper outputSchemaMapper,
OutputSelectionsMapper outputSelectionsMapper,
CompoundPropertiesMapper compoundPropertiesMapper,
ParameterMapper parameterMapper,
AdvancedParameterMapper advancedParameterMapper,
EventMappingMapper eventMappingMapper,
ObserverSetMappingMapper observerSetMappingMapper,
SimulationTimeProfileChartMapper simulationTimeProfileChartMapper,
PopulationAnalysisChartMapper populationAnalysisChartMapper,
ProcessMappingMapper processMappingMapper,
ISimulationFactory simulationFactory,
IExecutionContext executionContext,
ISimulationModelCreator simulationModelCreator,
ISimulationBuildingBlockUpdater simulationBuildingBlockUpdater,
IModelPropertiesTask modelPropertiesTask,
ISimulationRunner simulationRunner,
ISimulationParameterOriginIdUpdater simulationParameterOriginIdUpdater,
ILogger logger,
IContainerTask containerTask,
IEntityPathResolver entityPathResolver
)
{
_solverSettingsMapper = solverSettingsMapper;
_outputSchemaMapper = outputSchemaMapper;
_outputSelectionsMapper = outputSelectionsMapper;
_compoundPropertiesMapper = compoundPropertiesMapper;
_parameterMapper = parameterMapper;
_advancedParameterMapper = advancedParameterMapper;
_eventMappingMapper = eventMappingMapper;
_observerSetMappingMapper = observerSetMappingMapper;
_simulationTimeProfileChartMapper = simulationTimeProfileChartMapper;
_populationAnalysisChartMapper = populationAnalysisChartMapper;
_processMappingMapper = processMappingMapper;
_simulationFactory = simulationFactory;
_executionContext = executionContext;
_simulationModelCreator = simulationModelCreator;
_simulationBuildingBlockUpdater = simulationBuildingBlockUpdater;
_modelPropertiesTask = modelPropertiesTask;
_simulationRunner = simulationRunner;
_simulationParameterOriginIdUpdater = simulationParameterOriginIdUpdater;
_logger = logger;
_containerTask = containerTask;
_entityPathResolver = entityPathResolver;
}
protected override void Context()
{
_parameter = DomainHelperForSpecs.ConstantParameterWithValue(10);
_formulaTypeMapper = A.Fake <IFormulaToFormulaTypeMapper>();
_representationInfoRepository = A.Fake <IRepresentationInfoRepository>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_favoriteRepository = A.Fake <IFavoriteRepository>();
_pathToPathElementsMapper = A.Fake <IPathToPathElementsMapper>();
_parameterListOfValuesRetriever = A.Fake <IParameterListOfValuesRetriever>();
sut = new ParameterToParameterDTOMapper(
_representationInfoRepository,
_formulaTypeMapper,
_pathToPathElementsMapper,
_favoriteRepository,
_entityPathResolver,
_parameterListOfValuesRetriever);
}
protected IndividualMoleculeFactory(
IObjectBaseFactory objectBaseFactory,
IParameterFactory parameterFactory,
IObjectPathFactory objectPathFactory,
IEntityPathResolver entityPathResolver,
IIdGenerator idGenerator,
IParameterRateRepository parameterRateRepository,
string containerPath)
{
_objectBaseFactory = objectBaseFactory;
_parameterFactory = parameterFactory;
_objectPathFactory = objectPathFactory;
_entityPathResolver = entityPathResolver;
_idGenerator = idGenerator;
_parameterRateRepository = parameterRateRepository;
_containerPath = containerPath;
}
public IndividualExtractor(
IExecutionContext executionContext,
IEntityPathResolver entityPathResolver,
IIndividualTask individualTask,
IContainerTask containerTask,
IBuildingBlockRepository buildingBlockRepository,
IGenderRepository genderRepository,
IPopulationRepository populationRepository)
{
_executionContext = executionContext;
_entityPathResolver = entityPathResolver;
_individualTask = individualTask;
_containerTask = containerTask;
_buildingBlockRepository = buildingBlockRepository;
_genderRepository = genderRepository;
_populationRepository = populationRepository;
}
protected override void Context()
{
_view = A.Fake <IEditFavoritesView>();
_editParameterListPresenter = A.Fake <IEditParameterListPresenter>();
_favoriteRepository = A.Fake <IFavoriteRepository>();
_entityPathResolver = new EntityPathResolver(new ObjectPathFactory(A.Fake <IAliasCreator>()));
_favoriteTask = A.Fake <IFavoriteTask>();
sut = new EditFavoritesInSpatialStructurePresenter(_view, _favoriteRepository, _entityPathResolver, _editParameterListPresenter, _favoriteTask);
_spatialStructure = new MoBiSpatialStructure();
var cont = new Container().WithName("root");
_para = new Parameter().WithName("P").WithParentContainer(cont);
_fav = new Parameter().WithName("F").WithParentContainer(cont);
_spatialStructure.AddTopContainer(cont);
A.CallTo(() => _favoriteRepository.All()).Returns(new[] { _entityPathResolver.PathFor(_fav) });
}
public DistributedParameterToTableParameterConverter(IFormulaFactory formulaFactory, IEntityPathResolver entityPathResolver, IParameterFactory parameterFactory,
ICloneManager cloneManager, IParameterQuery parameterQuery, IDimensionRepository dimensionRepository, IOntogenyRepository ontogenyRepository,
IFullPathDisplayResolver fullPathDisplayResolver, IInterpolation interpolation, IParameterStartValuesCreator parameterStartValuesCreator, IObjectPathFactory objectPathFactory)
{
_formulaFactory = formulaFactory;
_entityPathResolver = entityPathResolver;
_parameterFactory = parameterFactory;
_cloneManager = cloneManager;
_parameterQuery = parameterQuery;
_dimensionRepository = dimensionRepository;
_ontogenyRepository = ontogenyRepository;
_fullPathDisplayResolver = fullPathDisplayResolver;
_interpolation = interpolation;
_parameterStartValuesCreator = parameterStartValuesCreator;
_objectPathFactory = objectPathFactory;
_timeDimension = dimensionRepository.Time;
_yearUnit = _timeDimension.Unit(dimensionRepository.AgeInYears.BaseUnit.Name);
}
protected override void Context()
{
_entityPathResolver = A.Fake <IEntityPathResolver>();
_fullPathDisplayResolver = A.Fake <IFullPathDisplayResolver>();
_parameter = A.Fake <IParameter>();
_genderRepository = A.Fake <IGenderRepository>();
_male = new Gender {
DisplayName = "Male"
};
_female = new Gender {
DisplayName = "Female"
};
A.CallTo(() => _genderRepository.Male).Returns(_male);
A.CallTo(() => _genderRepository.Female).Returns(_female);
_colorGenerator = A.Fake <IColorGenerator>();
_pkParameterRepository = A.Fake <IPKParameterRepository>();
sut = new PopulationAnalysisFieldFactory(_entityPathResolver, _fullPathDisplayResolver, _genderRepository, _colorGenerator, _pkParameterRepository);
}
public SimulationModelCreator(IBuildConfigurationTask buildConfigurationTask,
IModelConstructor modelConstructor,
IParameterIdUpdater parameterIdUpdater,
ISimulationSettingsFactory simulationSettingsFactory,
ISimulationPersistableUpdater simulationPersistableUpdater,
ISimulationConfigurationValidator simulationConfigurationValidator,
IEntityPathResolver entityPathResolver,
IContainerTask containerTask)
{
_buildConfigurationTask = buildConfigurationTask;
_modelConstructor = modelConstructor;
_parameterIdUpdater = parameterIdUpdater;
_simulationSettingsFactory = simulationSettingsFactory;
_simulationPersistableUpdater = simulationPersistableUpdater;
_simulationConfigurationValidator = simulationConfigurationValidator;
_entityPathResolver = entityPathResolver;
_containerTask = containerTask;
}
protected AdvancedParameterDistributionPresenter(IAdvancedParameterDistributionView view, IPopulationParameterGroupsPresenter parametersPresenter,
IRepresentationInfoRepository representationInfoRepository, IEntityPathResolver entityPathResolver, IPopulationDistributionPresenter populationParameterDistributionPresenter,
IProjectChangedNotifier projectChangedNotifier)
: base(view)
{
_parametersPresenter = parametersPresenter;
_representationInfoRepository = representationInfoRepository;
_entityPathResolver = entityPathResolver;
_populationParameterDistributionPresenter = populationParameterDistributionPresenter;
_projectChangedNotifier = projectChangedNotifier;
_defaultSettings = new DistributionSettings();
_parametersPresenter.GroupNodeSelected += (o, e) => activateNode(e.Node);
_parametersPresenter.ParameterNodeSelected += (o, e) => activateNode(e.Node);
_view.UpdateParameterGroupView(_parametersPresenter.View);
_allParametersCache = new PathCache <IParameter>(_entityPathResolver);
_view.AddDistributionView(_populationParameterDistributionPresenter.View);
AddSubPresenters(_parametersPresenter, _populationParameterDistributionPresenter);
}
protected override void Context()
{
_entityPathResolver = new EntityPathResolverForSpecs();
_representationInfoRepository = new RepresentationInfoRepositoryForSpecs();
sut = new PKSimPathToPathElementsMapper(_representationInfoRepository, _entityPathResolver);
_organism = new Organism();
_venousBlood = new Organ().WithName(CoreConstants.Organ.VenousBlood).WithParentContainer(_organism);
_liver = new Organ().WithName(CoreConstants.Organ.Liver).WithParentContainer(_organism);
_kidney = new Organ().WithName(CoreConstants.Organ.Kidney).WithParentContainer(_organism);
_liverInt = new Compartment().WithName(CoreConstants.Compartment.Interstitial).WithParentContainer(_liver);
_liverCell = new Compartment().WithName(CoreConstants.Compartment.Intracellular).WithParentContainer(_liver);
_kidneyUrine = new Compartment().WithName(CoreConstants.Compartment.URINE).WithParentContainer(_kidney);
_gallBladder = new Organ().WithName(CoreConstants.Organ.Gallbladder).WithParentContainer(_organism);
_lumen = new Organ().WithName(CoreConstants.Organ.Lumen).WithParentContainer(_organism);
_peripheralVenousBlood = new Container().WithName(CoreConstants.Organ.PeripheralVenousBlood).WithParentContainer(_organism);
_smallIntestine = new Organ().WithName(CoreConstants.Organ.SmallIntestine).WithParentContainer(_organism);
_mucosa = new Compartment().WithName(CoreConstants.Compartment.Mucosa).WithParentContainer(_smallIntestine);
_mucosa_duo = new Compartment().WithName(CoreConstants.Compartment.Duodenum).WithParentContainer(_mucosa);
_mucosa_duo_interstitial = new Compartment().WithName(CoreConstants.Compartment.Interstitial).WithParentContainer(_mucosa_duo);
_events = new Container().WithName(Constants.EVENTS);
_eventGroup = new EventGroup().WithName("E1").WithParentContainer(_events);
_plasma = new Compartment().WithName(CoreConstants.Compartment.Plasma).WithParentContainer(_venousBlood);
_drugContainerVenousBlood = new Container().WithName(_drugName).WithContainerType(ContainerType.Molecule).WithParentContainer(_venousBlood);
_drugContainerPeripheralVenousBlood = new Container().WithName(_drugName).WithContainerType(ContainerType.Molecule).WithParentContainer(_peripheralVenousBlood);
_drugContainerGallBladder = new Container().WithName(_drugName).WithContainerType(ContainerType.Molecule).WithParentContainer(_gallBladder);
_drugContainerInLumen = new Container().WithName(_drugName).WithContainerType(ContainerType.Molecule).WithParentContainer(_lumen);
_drugContainerInLiverCell = new Container().WithName(_drugName).WithContainerType(ContainerType.Molecule).WithParentContainer(_liverCell);
_drug = new MoleculeAmount().WithName(_drugName).WithParentContainer(_plasma);
_drugUrineKidney = new MoleculeAmount().WithName(_drugName).WithParentContainer(_kidneyUrine);
_applications = new Container().WithName(Constants.APPLICATIONS);
_application1 = new EventGroup().WithName("App").WithParentContainer(_applications).WithContainerType(ContainerType.EventGroup);
_formulation = new Container().WithName("F1").WithParentContainer(_application1);
_neighborhoods = new Container().WithName(Constants.NEIGHBORHOODS);
_liverCellToLiverIntNeighborhood = new Neighborhood {
FirstNeighbor = _liverInt, SecondNeighbor = _liverCell
}.WithParentContainer(_neighborhoods);
_concentrationDimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
_fractionDimension = DomainHelperForSpecs.FractionDimensionForSpecs();
}
protected override void Context()
{
_configuration = A.Fake <IPKSimConfiguration>();
_applicationController = A.Fake <IApplicationController>();
_workspace = A.Fake <IWorkspace>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_selectFilePresenter = A.Fake <ISelectFilePresenter>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
_simModelExporter = A.Fake <ISimModelExporter>();
_modelCoreSimulationMapper = A.Fake <ISimulationToModelCoreSimulationMapper>();
_simulationSettingsRetriever = A.Fake <ISimulationSettingsRetriever>();
_dialogCreator = A.Fake <IDialogCreator>();
_cloner = A.Fake <ICloner>();
_population = A.Fake <Population>().WithName("MyPop");
A.CallTo(() => _population.AllCovariateNames).Returns(new[] { CoreConstants.Covariates.GENDER, CoreConstants.Covariates.RACE });
A.CallTo(() => _applicationController.Start <ISelectFilePresenter>()).Returns(_selectFilePresenter);
sut = new PopulationExportTask(_applicationController, _entityPathResolver, _lazyLoadTask, _simModelExporter,
_modelCoreSimulationMapper, _workspace, _configuration, _simulationSettingsRetriever, _dialogCreator, _cloner);
}
protected override void Context()
{
_context = A.Fake <IMoBiContext>();
_liver = new Container().WithName("LIVER");
_simulation = A.Fake <IMoBiSimulation>();
_simulation.Model.Root = new Container().WithContainerType(ContainerType.Simulation);
_simulation.Model.Root.Add(_liver);
_moleculeStartValues = new MoleculeStartValuesBuildingBlock();
_simulation.BuildConfiguration.MoleculeStartValues = _moleculeStartValues;
sut = new ResetMoleculeValuesToDefaultFromStartValuesInSimulationCommand(_simulation);
_formulaTask = A.Fake <IMoBiFormulaTask>();
_entityPathResolver = new EntityPathResolver(new ObjectPathFactory(new AliasCreator()));
_cloneManagerForModel = A.Fake <ICloneManagerForModel>();
A.CallTo(_formulaTask).WithReturnType <ConstantFormula>().Returns(new ConstantFormula());
A.CallTo(() => _context.Resolve <IMoBiFormulaTask>()).Returns(_formulaTask);
A.CallTo(() => _context.Resolve <IEntityPathResolver>()).Returns(_entityPathResolver);
A.CallTo(() => _context.Resolve <ICloneManagerForModel>()).Returns(_cloneManagerForModel);
}
public SimulationExpressionsPresenter(
ISimulationExpressionsView view,
IExpressionParametersToSimulationExpressionsDTOMapper simulationExpressionsDTOMapper,
IEditParameterPresenterTask editParameterPresenterTask,
IMoleculeExpressionTask <Individual> moleculeExpressionTask,
IEntityPathResolver entityPathResolver,
IParameterTask parameterTask,
IMultiParameterEditPresenter moleculeParametersPresenter)
: base(view, editParameterPresenterTask)
{
_simulationExpressionsDTOMapper = simulationExpressionsDTOMapper;
_moleculeExpressionTask = moleculeExpressionTask;
_parameterTask = parameterTask;
_pathCache = new PathCache <IParameter>(entityPathResolver);
_moleculeParametersPresenter = moleculeParametersPresenter;
_moleculeParametersPresenter.IsSimpleEditor = true;
AddSubPresenters(moleculeParametersPresenter);
view.AddMoleculeParametersView(_moleculeParametersPresenter.View);
}
protected override Task Context()
{
_tableFormulaMapper = A.Fake <TableFormulaMapper>();
_valueOriginMapper = A.Fake <ValueOriginMapper>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_logger = A.Fake <IOSPSuiteLogger>();
_containerTask = new ContainerTaskForSpecs();
sut = new ParameterMapper(_tableFormulaMapper, _valueOriginMapper, _entityPathResolver, _logger, _containerTask);
//5 mm is the value
_parameter = DomainHelperForSpecs.ConstantParameterWithValue(10)
.WithName("P1")
.WithDescription("P1 description")
.WithDimension(DomainHelperForSpecs.LengthDimensionForSpecs());
_parameter.DisplayUnit = _parameter.Dimension.Unit("mm");
_snapshotValueOrigin = new ValueOrigin();
A.CallTo(() => _valueOriginMapper.MapToSnapshot(_parameter.ValueOrigin)).Returns(_snapshotValueOrigin);
return(_completed);
}
protected override void Context()
{
_parameterIdentificationFactory = A.Fake <IParameterIdentificationFactory>();
_withIdRepository = A.Fake <IWithIdRepository>();
_entitiesInSimulationRetriever = A.Fake <IEntitiesInSimulationRetriever>();
_observedDataRepository = A.Fake <IObservedDataRepository>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_identificationParameterFactory = A.Fake <IIdentificationParameterFactory>();
_executionContext = A.Fake <IOSPSuiteExecutionContext>();
_favoriteRepository = A.Fake <IFavoriteRepository>();
_simulationSwapValidator = A.Fake <IParameterIdentificationSimulationSwapValidator>();
_applicationController = A.Fake <IApplicationController>();
_simulationSwapCorrector = A.Fake <IParameterIdentificationSimulationSwapCorrector>();
_dialogCreator = A.Fake <IDialogCreator>();
_simulationSelector = A.Fake <ISimulationSelector>();
_parameterAnalysableParameterSelector = A.Fake <IParameterAnalysableParameterSelector>();
_heavyWorkManager = new HeavyWorkManagerForSpecs();
sut = new ParameterIdentificationTask(_parameterIdentificationFactory, _withIdRepository, _entitiesInSimulationRetriever, _observedDataRepository,
_entityPathResolver, _identificationParameterFactory, _executionContext, _favoriteRepository, _simulationSwapValidator, _applicationController,
_simulationSwapCorrector, _dialogCreator, _simulationSelector, _heavyWorkManager, _parameterAnalysableParameterSelector);
}
protected override void Context()
{
_executionContext = A.Fake <IExecutionContext>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_individualTask = A.Fake <IIndividualTask>();
_containerTask = new ContainerTaskForSpecs();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_genderRepository = A.Fake <IGenderRepository>();
_populationRepository = A.Fake <IPopulationRepository>();
sut = new IndividualExtractor(
_executionContext,
_entityPathResolver,
_individualTask,
_containerTask,
_buildingBlockRepository,
_genderRepository,
_populationRepository);
_templateIndividual1 = new Individual();
A.CallTo(() => _buildingBlockRepository.All <Individual>()).Returns(new[] { _templateIndividual1 });
}
protected override void Context()
{
_compartment = A.Fake <Compartment>();
A.CallTo(() => _compartment.OrganName).Returns("MyParentOrgan");
_compartment.Name = "MyComp";
var containerPath = new ObjectPath(new[] { _compartment.OrganName, _compartment.Name }).ToString();
_containerPathRetriever = A.Fake <IEntityPathResolver>();
A.CallTo(() => _containerPathRetriever.PathFor(_compartment)).Returns(containerPath);
_originData = new OriginData();
_originData.Population = new SpeciesPopulation();
var distributionDefinition = new ParameterDistributionMetaData();
var rateDefinition = new ParameterRateMetaData();
var valueDefinition = new ParameterValueMetaData();
distributionDefinition.ParameterName = "tutu";
var distributionRepository = A.Fake <IParameterDistributionRepository>();
A.CallTo(() => distributionRepository.AllFor(containerPath)).Returns(new List <ParameterDistributionMetaData> {
distributionDefinition
});
var rateRepository = A.Fake <IParameterRateRepository>();
A.CallTo(() => rateRepository.AllFor(containerPath)).Returns(new List <ParameterRateMetaData> {
rateDefinition
});
var valueRepository = A.Fake <IParameterValueRepository>();
A.CallTo(() => valueRepository.AllFor(containerPath)).Returns(new List <ParameterValueMetaData> {
valueDefinition
});
sut = new ParameterQuery(distributionRepository, valueRepository, rateRepository, _containerPathRetriever);
}
