protected override void Context()
{
base.Context();
_simulationFactory = IoC.Resolve <ISimulationFactory>();
_buildConfigurationFactory = IoC.Resolve <IBuildConfigurationFactory>();
_modelConstructor = IoC.Resolve <IModelConstructor>();
_simulationSettingsFactory = IoC.Resolve <ISimulationSettingsFactory>();
_observerBuilder = IoC.Resolve <IObserverBuilder>();
_fileName = Helper.TestFileFullPath("tiny_example_12.xml");
}
public ImportSimulationTask(ISimulationTransferLoader simulationTransferLoader, ISimulationFactory simulationFactory, IEntitiesInContainerRetriever parameterRetriever, ISimulationBuildingBlockUpdater simulationBuildingBlockUpdater,
IIndividualPropertiesCacheImporter individualPropertiesCacheImporter, IExecutionContext executionContext, IObjectBaseFactory objectBaseFactory,
ISimulationUpdaterAfterDeserialization simulationUpdaterAfterDeserialization, IAdvancedParameterFactory advancedParameterFactory)
{
_simulationTransferLoader = simulationTransferLoader;
_simulationFactory = simulationFactory;
_parameterRetriever = parameterRetriever;
_simulationBuildingBlockUpdater = simulationBuildingBlockUpdater;
_individualPropertiesCacheImporter = individualPropertiesCacheImporter;
_executionContext = executionContext;
_objectBaseFactory = objectBaseFactory;
_simulationUpdaterAfterDeserialization = simulationUpdaterAfterDeserialization;
_advancedParameterFactory = advancedParameterFactory;
}
public Broker(ILogger logger, ISimulationFactory simulationFactory, IGeneric generic)
{
Logger = logger;
_simulationFactory = simulationFactory;
Generic = generic;
Port = -1;
_callbackMap = new Dictionary <string, Func <int, HttpListenerContext, HttpResponseMessage> >
{
{ "register", RegisterCallback },
{ "pact", PactCallback },
{ "redirect", RedirectCallback },
{ "log", LogCallback }
};
}
protected override void Context()
{
_simulationTransferLoader = A.Fake <ISimulationTransferLoader>();
_simulationFactory = A.Fake <ISimulationFactory>();
_parameterRetriever = A.Fake <IEntitiesInContainerRetriever>();
_simulationBuildingBlockUpdater = A.Fake <ISimulationBuildingBlockUpdater>();
_executionContext = A.Fake <IExecutionContext>();
_individualPropertiesCacheImporter = A.Fake <IIndividualPropertiesCacheImporter>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_simulationUpdaterAfterDeserialization = A.Fake <ISimulationUpdaterAfterDeserialization>();
_advancedParameterFactory = A.Fake <IAdvancedParameterFactory>();
sut = new ImportSimulationTask(_simulationTransferLoader, _simulationFactory, _parameterRetriever,
_simulationBuildingBlockUpdater, _individualPropertiesCacheImporter, _executionContext, _objectBaseFactory,
_simulationUpdaterAfterDeserialization, _advancedParameterFactory);
}
public ProjectComparisonRunner(IWorkspacePersistor workspacePersistor, IWorkspace workspace,
ILazyLoadTask lazyLoadTask, IBatchLogger logger, ISimulationEngineFactory simulationEngineFactory, ISimulationExportTask simulationExportTask,
IMoBiExportTask moBiExportTask, ISimulationFactory simulationFactory, IExecutionContext executionContext, ISimulationModelCreator simulationModelCreator)
{
_workspacePersistor = workspacePersistor;
_workspace = workspace;
_lazyLoadTask = lazyLoadTask;
_logger = logger;
_simulationExportTask = simulationExportTask;
_moBiExportTask = moBiExportTask;
_simulationFactory = simulationFactory;
_executionContext = executionContext;
_simulationModelCreator = simulationModelCreator;
_simulationEngine = simulationEngineFactory.Create <IndividualSimulation>();
}
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()
{
_context = A.Fake <IMoBiContext>();
_serializationTask = A.Fake <ISerializationTask>();
_dialogCreator = A.Fake <IDialogCreator>();
_buildConfigurationMapper = A.Fake <IBuildConfigurationToMoBiBuildconfigurationMapper>();
_nameCorrector = A.Fake <INameCorrector>();
_mruProvider = A.Fake <IMRUProvider>();
_spatialStructureFactory = A.Fake <IMoBiSpatialStructureFactory>();
_simFactory = A.Fake <ISimulationFactory>();
_cloneManager = A.Fake <ICloneManagerForSimulation>();
_simSettingsFactory = A.Fake <ISimulationSettingsFactory>();
_appController = A.Fake <IMoBiApplicationController>();
_sbmlTask = A.Fake <ISbmlTask>();
_reactionBuildingBlockFactory = A.Fake <IReactionBuildingBlockFactory>();
sut = new ProjectTask(_context, _serializationTask, _dialogCreator, _mruProvider, _spatialStructureFactory, new HeavyWorkManagerForSpecs(),
_simSettingsFactory, new SimulationLoader(_cloneManager, _nameCorrector, _context), _sbmlTask, _reactionBuildingBlockFactory);
}
protected override void Context()
{
_defaultIndividualRetriever = A.Fake <IDefaultIndividualRetriever>();
_speciesRepository = A.Fake <ISpeciesRepository>();
_simulationFactory = A.Fake <ISimulationFactory>();
_parameterFactory = A.Fake <IParameterFactory>();
_protocolFactory = A.Fake <IProtocolFactory>();
sut = new VSSCalculator(_defaultIndividualRetriever, _speciesRepository, _simulationFactory, _parameterFactory, _protocolFactory);
_species1 = new Species().WithId("Human");
_species2 = new Species().WithId("Dog");
A.CallTo(() => _speciesRepository.All()).Returns(new[] { _species1, _species2 });
_simulation = A.Fake <Simulation>();
var organism = new Organism();
organism.Add(DomainHelperForSpecs.ConstantParameterWithValue(0.5).WithName(CoreConstants.Parameter.HCT));
A.CallTo(() => _simulation.Individual.Organism).Returns(organism);
}
public CreateSimulationPresenter(
ICreateSimulationView view,
IMoBiContext context,
IModelConstructor modelConstructor,
IDimensionValidator dimensionValidator,
ISimulationFactory simulationFactory,
IBuildConfigurationFactory buildConfigurationFactory,
IHeavyWorkManager heavyWorkManager,
ISubPresenterItemManager <ISimulationItemPresenter> subPresenterManager,
IDialogCreator dialogCreator,
IForbiddenNamesRetriever forbiddenNamesRetriever,
IUserSettings userSettings)
: base(view, subPresenterManager, dialogCreator, buildConfigurationFactory, context, SimulationItems.All)
{
_simulationFactory = simulationFactory;
_heavyWorkManager = heavyWorkManager;
_forbiddenNamesRetriever = forbiddenNamesRetriever;
_userSettings = userSettings;
_dimensionValidator = dimensionValidator;
_modelConstructor = modelConstructor;
}
protected override void Context()
{
_simulationPresenter = A.Fake <ICreateSimulationPresenter>();
_view = A.Fake <ISimulationSubjectConfigurationView>();
_simulationFactory = A.Fake <ISimulationFactory>();
_buildingBlockInSimulationManager = A.Fake <IBuildingBlockInSimulationManager>();
_simulation = A.Fake <Simulation>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
sut = new SimulationSubjectConfigurationPresenter(_view, _lazyLoadTask, _buildingBlockInSimulationManager);
A.CallTo(() => _view.BindTo(A <SimulationSubjectDTO> ._))
.Invokes(x => _simulationSubjectDTO = x.GetArgument <SimulationSubjectDTO>(0));
sut.InitializeWith(_simulationPresenter);
_subject = A.Fake <ISimulationSubject>();
var originData = new OriginData {
SpeciesPopulation = A.Fake <SpeciesPopulation>()
};
A.CallTo(() => _subject.OriginData).Returns(originData);
sut.Initialize();
}
public GlobalPKAnalysisRunner(ISimulationEngine <IndividualSimulation> simulationEngine, ISimulationFactory simulationFactory, IRegistrationTask registrationTask)
{
_simulationEngine = simulationEngine;
_simulationFactory = simulationFactory;
_registrationTask = registrationTask;
}
protected override Task Context()
{
_solverSettingsMapper = A.Fake <SolverSettingsMapper>();
_outputSchemaMapper = A.Fake <OutputSchemaMapper>();
_outputSelectionMapper = A.Fake <OutputSelectionsMapper>();
_parameterMapper = A.Fake <ParameterMapper>();
_compoundPropertiesMapper = A.Fake <CompoundPropertiesMapper>();
_advancedParameterMapper = A.Fake <AdvancedParameterMapper>();
_eventMappingMapper = A.Fake <EventMappingMapper>();
_observerSetMappingMapper = A.Fake <ObserverSetMappingMapper>();
_curveChartMapper = A.Fake <SimulationTimeProfileChartMapper>();
_processMappingMapper = A.Fake <ProcessMappingMapper>();
_simulationFactory = A.Fake <ISimulationFactory>();
_executionContext = A.Fake <IExecutionContext>();
_simulationModelCreator = A.Fake <ISimulationModelCreator>();
_simulationBuildingBlockUpdater = A.Fake <ISimulationBuildingBlockUpdater>();
_modelPropertiesTask = A.Fake <IModelPropertiesTask>();
_simulationRunner = A.Fake <ISimulationRunner>();
_populationAnalysisChartMapper = A.Fake <PopulationAnalysisChartMapper>();
_simulationParameterOriginIdUpdater = A.Fake <ISimulationParameterOriginIdUpdater>();
_logger = A.Fake <ILogger>();
_containerTask = A.Fake <IContainerTask>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
sut = new SimulationMapper(_solverSettingsMapper, _outputSchemaMapper,
_outputSelectionMapper, _compoundPropertiesMapper, _parameterMapper,
_advancedParameterMapper, _eventMappingMapper, _observerSetMappingMapper, _curveChartMapper,
_populationAnalysisChartMapper, _processMappingMapper,
_simulationFactory, _executionContext, _simulationModelCreator,
_simulationBuildingBlockUpdater, _modelPropertiesTask,
_simulationRunner, _simulationParameterOriginIdUpdater,
_logger, _containerTask, _entityPathResolver
);
_project = new PKSimProject();
_individual = new Individual {
Name = "IND", Id = "IND"
};
_compound = new Compound {
Name = "COMP", Id = "COMP"
};
_observerSet = new ObserverSet {
Name = "OBS_SET", Id = "OBS_SET"
};
_protocol = new SimpleProtocol {
Name = "PROT", Id = "PROT"
};
_inductionProcess = new InductionProcess().WithName("Interaction process");
_compound.AddProcess(_inductionProcess);
_event = new PKSimEvent {
Name = "Event"
};
_population = new RandomPopulation()
{
Name = "POP"
};
_observedData = new DataRepository("OBS_ID").WithName("OBS");
_project.AddBuildingBlock(_individual);
_project.AddBuildingBlock(_compound);
_project.AddBuildingBlock(_event);
_project.AddBuildingBlock(_population);
_project.AddBuildingBlock(_observerSet);
_project.AddObservedData(_observedData);
_simulationProperties = new SimulationProperties
{
ModelProperties = new ModelProperties
{
ModelConfiguration = new ModelConfiguration {
ModelName = "4Comp"
}
}
};
_interactionSelection = new InteractionSelection {
ProcessName = _inductionProcess.Name
};
_noInteractionSelection = new InteractionSelection {
MoleculeName = "CYP2D6"
};
_simulationProperties.InteractionProperties.AddInteraction(_interactionSelection);
_simulationProperties.InteractionProperties.AddInteraction(_noInteractionSelection);
_settings = new SimulationSettings();
_rootContainer = new Container().WithName("Sim");
_model = new OSPSuite.Core.Domain.Model {
Root = _rootContainer
};
_individualSimulation = new IndividualSimulation
{
Name = "S1",
Properties = _simulationProperties,
SimulationSettings = _settings,
Description = "Simulation Description",
Model = _model
};
_simulationTimeProfile = new SimulationTimeProfileChart();
_snapshotSimulationTimeProfile = new CurveChart();
_individualSimulation.AddAnalysis(_simulationTimeProfile);
A.CallTo(() => _curveChartMapper.MapToSnapshot(_simulationTimeProfile)).Returns(_snapshotSimulationTimeProfile);
_populationSimulation = new PopulationSimulation
{
Properties = _simulationProperties,
SimulationSettings = _settings,
Model = _model
};
_advancedParameterCollection = new AdvancedParameterCollection();
_populationSimulationAnalysisChart = new BoxWhiskerAnalysisChart();
_populationSimulation.SetAdvancedParameters(_advancedParameterCollection);
_populationSimulation.AddAnalysis(_populationSimulationAnalysisChart);
_populationSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("IndTemplateId", PKSimBuildingBlockType.Individual)
{
BuildingBlock = _individual
});
_snapshotPopulationAnalysisChart = new Snapshots.PopulationAnalysisChart();
A.CallTo(() => _populationAnalysisChartMapper.MapToSnapshot(_populationSimulationAnalysisChart)).Returns(_snapshotPopulationAnalysisChart);
_snapshotInteraction = new CompoundProcessSelection();
A.CallTo(() => _processMappingMapper.MapToSnapshot(_interactionSelection)).Returns(_snapshotInteraction);
_snapshotInteraction.CompoundName = _compound.Name;
_snapshotInteraction.Name = _inductionProcess.Name;
_noSelectionSnapshotInteraction = new CompoundProcessSelection();
A.CallTo(() => _processMappingMapper.MapToSnapshot(_noInteractionSelection)).Returns(_noSelectionSnapshotInteraction);
_noSelectionSnapshotInteraction.MoleculeName = _noInteractionSelection.MoleculeName;
_compoundProperties = new CompoundProperties();
_snapshotCompoundProperties = new Snapshots.CompoundProperties {
Name = _compound.Name
};
_individualSimulation.Properties.AddCompoundProperties(_compoundProperties);
_eventMapping = new EventMapping();
_individualSimulation.EventProperties.AddEventMapping(_eventMapping);
_observerSetMapping = new ObserverSetMapping();
_individualSimulation.ObserverSetProperties.AddObserverSetMapping(_observerSetMapping);
A.CallTo(() => _compoundPropertiesMapper.MapToSnapshot(_compoundProperties, _project)).Returns(_snapshotCompoundProperties);
_eventSelection = new EventSelection
{
Name = _event.Name,
};
_observerSetSelection = new ObserverSetSelection
{
Name = _observerSet.Name,
};
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("IndTemplateId", PKSimBuildingBlockType.Individual)
{
BuildingBlock = _individual,
Altered = true
});
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("CompTemplateId", PKSimBuildingBlockType.Compound)
{
BuildingBlock = _compound
});
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("ProtTemplateId", PKSimBuildingBlockType.Protocol)
{
BuildingBlock = _protocol
});
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("ObserveSetTemplateId", PKSimBuildingBlockType.ObserverSet)
{
BuildingBlock = _observerSet
});
_populationSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("PopTemplateId", PKSimBuildingBlockType.Population)
{
BuildingBlock = _population
});
_individualSimulation.AddUsedObservedData(_observedData);
A.CallTo(() => _eventMappingMapper.MapToSnapshot(_eventMapping, _project)).Returns(_eventSelection);
A.CallTo(() => _observerSetMappingMapper.MapToSnapshot(_observerSetMapping, _project)).Returns(_observerSetSelection);
_outputSelectionSnapshot = new OutputSelections();
A.CallTo(() => _outputSelectionMapper.MapToSnapshot(_individualSimulation.OutputSelections)).Returns(_outputSelectionSnapshot);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotInteraction, _inductionProcess)).Returns(_interactionSelection);
return(_completed);
}
public SimulationModelConfigurationPresenter(ISimulationModelConfigurationView view, ISubPresenterItemManager <ISimulationModelConfigurationItemPresenter> subPresenterItemManager,
ISimulationFactory simulationFactory)
: base(view, subPresenterItemManager, SimulationModelConfigurationItems.All)
{
_simulationFactory = simulationFactory;
}
public CloneManagerForSimulation(ICloneManagerForBuildingBlock cloneManagerForBuildingBlock, ICloneManagerForModel cloneManagerForModel, ISimulationFactory simulationFactory)
{
_cloneManagerForBuildingBlock = cloneManagerForBuildingBlock;
_cloneManagerForModel = cloneManagerForModel;
_simulationFactory = simulationFactory;
}
public GlobalPKAnalysisRunner(ISimulationRunner simulationRunner, ISimulationFactory simulationFactory, IRegistrationTask registrationTask)
{
_simulationRunner = simulationRunner;
_simulationFactory = simulationFactory;
_registrationTask = registrationTask;
}
