public IndividualTeXBuilder(IContainerTask containerTask, IFullPathDisplayResolver fullPathDisplayResolver,
ITeXBuilderRepository texBuilderRepository, IReportGenerator reportGenerator, ILazyLoadTask lazyLoadTask) : base(texBuilderRepository, reportGenerator, lazyLoadTask)
{
_containerTask = containerTask;
_fullPathDisplayResolver = fullPathDisplayResolver;
}
public CreateIndividualAlgorithm(IContainerTask containerTask, IReportGenerator reportGenerator)
{
_containerTask = containerTask;
_reportGenerator = reportGenerator;
}
public SimulationSettingsTask(IExecutionContext executionContext, IOutputIntervalFactory outputIntervalFactory, IContainerTask containerTask)
{
_executionContext = executionContext;
_outputIntervalFactory = outputIntervalFactory;
_containerTask = containerTask;
}
public OutputSchemaMapper(OutputIntervalMapper outputIntervalMapper, IOutputSchemaFactory outputSchemaFactory, IContainerTask containerTask)
{
_outputIntervalMapper = outputIntervalMapper;
_outputSchemaFactory = outputSchemaFactory;
_containerTask = containerTask;
}
protected override void Context()
{
_entityPathResolver = A.Fake <IEntityPathResolver>();
_containerTask = new ContainerTask(A.Fake <IObjectBaseFactory>(), _entityPathResolver);
sut = new IndividualToIndividualValuesMapper(_containerTask);
}
protected ObservedDataTask(IDialogCreator dialogCreator, IOSPSuiteExecutionContext executionContext, IDataRepositoryTask dataRepositoryTask, IContainerTask containerTask, IObjectTypeResolver objectTypeResolver)
{
_dialogCreator = dialogCreator;
_executionContext = executionContext;
_dataRepositoryTask = dataRepositoryTask;
_containerTask = containerTask;
_objectTypeResolver = objectTypeResolver;
}
public BuildingBlockParametersToSimulationUpdater(IExecutionContext executionContext, IContainerTask containerTask, IParameterSetUpdater parameterSetUpdater)
{
_executionContext = executionContext;
_containerTask = containerTask;
_parameterSetUpdater = parameterSetUpdater;
}
public CalculateScaleDivisorsPresenter(ICalculateScaleDivisorsView view, ICommandTask commandTask, IContainerTask containerTask,
IScaleDivisorCalculator scaleDivisorCalculator, IMoleculeAmountTask moleculeAmountTask, IMoBiContext context)
: base(view)
{
_commandTask = commandTask;
_containerTask = containerTask;
_scaleDivisorCalculator = scaleDivisorCalculator;
_moleculeAmountTask = moleculeAmountTask;
_context = context;
_commands = new MoBiMacroCommand
{
CommandType = AppConstants.Commands.EditCommand,
ObjectType = ObjectTypes.Simulation
};
}
public ScaleDivisorCalculator(ISimModelManager simModelManager, IContainerTask containerTask, IObjectPathFactory objectPathFactory)
{
_simModelManager = simModelManager;
_containerTask = containerTask;
_objectPathFactory = objectPathFactory;
}
public ObserverBuilderTask(IObserverBuilderToObserverMapper observerMapper, IContainerTask containerTask, IKeywordReplacerTask keywordReplacerTask)
{
_observerMapper = observerMapper;
_containerTask = containerTask;
_keywordReplacerTask = keywordReplacerTask;
}
public ParameterIdentificationFactory(IObjectBaseFactory objectBaseFactory, IOSPSuiteExecutionContext executionContext, IContainerTask containerTask)
{
_objectBaseFactory = objectBaseFactory;
_executionContext = executionContext;
_containerTask = containerTask;
}
public IdentificationParameterFactory(IObjectBaseFactory objectBaseFactory, IContainerTask containerTask, IIdentificationParameterTask identificationParameterTask)
{
_objectBaseFactory = objectBaseFactory;
_containerTask = containerTask;
_identificationParameterTask = identificationParameterTask;
}
protected ParameterAnalysableAnalysisCreator(IContainerTask containerTask, IOSPSuiteExecutionContext context, IObjectIdResetter objectIdResetter, IIdGenerator idGenerator) : base(containerTask, context)
{
_context = context;
_objectIdResetter = objectIdResetter;
_idGenerator = idGenerator;
}
protected override void Context()
{
var entityPathFactory = new EntityPathResolverForSpecs();
_objectPathFactory = new ObjectPathFactory(new AliasCreator());
_simulation = A.Fake <IModelCoreSimulation>().WithName("Sim");
_simModelManager = A.Fake <ISimModelManager>();
_containerTask = A.Fake <IContainerTask>();
_options = new ScaleDivisorOptions();
_moleculeAmountCache = new PathCache <IMoleculeAmount>(entityPathFactory);
var rootContainer = new ARootContainer().WithName(_simulation.Name)
.WithContainerType(ContainerType.Simulation);
_simulation.Model.Root = rootContainer;
_moleculeAmount1 = new MoleculeAmount().WithName("M1");
_moleculeAmount2 = new MoleculeAmount().WithName("M2");
rootContainer.Add(_moleculeAmount1);
rootContainer.Add(_moleculeAmount2);
_moleculeAmountCache.Add(_moleculeAmount1);
_moleculeAmountCache.Add(_moleculeAmount2);
_molecule1Path = entityPathFactory.PathFor(_moleculeAmount1);
_molecule2Path = entityPathFactory.PathFor(_moleculeAmount2);
_originalResults = new DataRepository();
_simulation.Results = _originalResults;
var baseGrid = new BaseGrid("Time", Constants.Dimension.NO_DIMENSION)
{
Values = new[] { 0f, 1f, 2f, 3f }
};
_originalDataColumn = new DataColumn("M1", Constants.Dimension.NO_DIMENSION, baseGrid)
{
Values = new[] { 0f, 10f, 20f, 30f }
};
_originalDataColumn.QuantityInfo.Path = _objectPathFactory.CreateAbsoluteObjectPath(_moleculeAmount1);
_originalResults.Add(_originalDataColumn);
A.CallTo(_containerTask).WithReturnType <PathCache <IMoleculeAmount> >().Returns(_moleculeAmountCache);
var simResults = new DataRepository();
var baseGrid2 = new BaseGrid("Time", Constants.Dimension.NO_DIMENSION)
{
Values = new[] { 0f, 1f, 2f, 3f }
};
var res1 = new DataColumn("M1", Constants.Dimension.NO_DIMENSION, baseGrid2)
{
Values = new[] { 0f, 10f, 20f, 30f }
};
res1.QuantityInfo.Path = _objectPathFactory.CreateAbsoluteObjectPath(_moleculeAmount1);
simResults.Add(res1);
var res2 = new DataColumn("M2", Constants.Dimension.NO_DIMENSION, baseGrid2)
{
Values = new[] { 0f, 11f, 12f, 13f }
};
res2.QuantityInfo.Path = _objectPathFactory.CreateAbsoluteObjectPath(_moleculeAmount2);
simResults.Add(res2);
var simulationRunResults = new SimulationRunResults(true, Enumerable.Empty <SolverWarning>(), simResults);
A.CallTo(() => _simModelManager.RunSimulation(_simulation)).Returns(simulationRunResults);
sut = new ScaleDivisorCalculator(_simModelManager, _containerTask, _objectPathFactory);
}
public IndividualToIndividualValuesMapper(IContainerTask containerTask)
{
_containerTask = containerTask;
}
public EntitiesInSimulationRetriever(IEntityPathResolver entityPathResolver, IContainerTask containerTask)
{
_entityPathResolver = entityPathResolver;
_containerTask = containerTask;
}
public Converter552To561(ICompoundCalculationMethodCategoryRepository compoundCalculationMethodCategoryRepository, IIndividualFactory individualFactory,
ICloner cloner, INeighborhoodFinalizer neighborhoodFinalizer, IContainerTask containerTask,
IPKSimXmlSerializerRepository serializerRepository, IReactionBuildingBlockCreator reactionBuildingBlockCreator,
IDiagramModelFactory diagramModelFactory, ICompoundProcessRepository compoundProcessRepository, IParameterSetUpdater parameterSetUpdater, IDialogCreator dialogCreator,
IIndividualCalculationMethodsUpdater individualCalculationMethodsUpdater,
IIndividualUpdater individualUpdater)
{
_compoundCalculationMethodCategoryRepository = compoundCalculationMethodCategoryRepository;
_individualFactory = individualFactory;
_cloner = cloner;
_neighborhoodFinalizer = neighborhoodFinalizer;
_containerTask = containerTask;
_serializerRepository = serializerRepository;
_reactionBuildingBlockCreator = reactionBuildingBlockCreator;
_diagramModelFactory = diagramModelFactory;
_compoundProcessRepository = compoundProcessRepository;
_parameterSetUpdater = parameterSetUpdater;
_dialogCreator = dialogCreator;
_individualCalculationMethodsUpdater = individualCalculationMethodsUpdater;
_individualUpdater = individualUpdater;
}
public SimulationParametersToBuildingBlockUpdater(IContainerTask containerTask, IParameterSetUpdater parameterSetUpdater, IExecutionContext executionContext)
{
_containerTask = containerTask;
_parameterSetUpdater = parameterSetUpdater;
_executionContext = executionContext;
}
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>();
_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, _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"
};
_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.AddObservedData(_observedData);
_simulationProperties = new SimulationProperties
{
ModelProperties = new ModelProperties
{
ModelConfiguration = new ModelConfiguration {
ModelName = "4Comp"
}
}
};
_intereactionSelection = new InteractionSelection {
ProcessName = _inductionProcess.Name
};
_simulationProperties.InteractionProperties.AddInteraction(_intereactionSelection);
_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
};
_avancedParameterCollection = new AdvancedParameterCollection();
_populationSimulationAnalysisChart = new BoxWhiskerAnalysisChart();
_populationSimulation.SetAdvancedParameters(_avancedParameterCollection);
_populationSimulation.AddAnalysis(_populationSimulationAnalysisChart);
_snapshotPopulationAnalysisChart = new Snapshots.PopulationAnalysisChart();
A.CallTo(() => _populationAnalysisChartMapper.MapToSnapshot(_populationSimulationAnalysisChart)).Returns(_snapshotPopulationAnalysisChart);
_snapshotInteraction = new CompoundProcessSelection();
A.CallTo(() => _processMappingMapper.MapToSnapshot(_intereactionSelection)).Returns(_snapshotInteraction);
_snapshotInteraction.CompoundName = _compound.Name;
_snapshotInteraction.Name = _inductionProcess.Name;
_compoundProperties = new CompoundProperties();
_snaphotCompoundProperties = new Snapshots.CompoundProperties {
Name = _compound.Name
};
_individualSimulation.Properties.AddCompoundProperties(_compoundProperties);
_eventMapping = new EventMapping();
_individualSimulation.EventProperties.AddEventMapping(_eventMapping);
A.CallTo(() => _compoundPropertiesMapper.MapToSnapshot(_compoundProperties, _project)).Returns(_snaphotCompoundProperties);
_eventSelection = new EventSelection
{
Name = _event.Name,
};
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("IndTemplateId", PKSimBuildingBlockType.Individual)
{
BuildingBlock = _individual
});
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("CompTemplateId", PKSimBuildingBlockType.Compound)
{
BuildingBlock = _compound
});
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("ProtTemplateId", PKSimBuildingBlockType.Protocol)
{
BuildingBlock = _protocol
});
_populationSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("PopTemplateId", PKSimBuildingBlockType.Population)
{
BuildingBlock = _population
});
_individualSimulation.AddUsedObservedData(_observedData);
A.CallTo(() => _eventMappingMapper.MapToSnapshot(_eventMapping, _project)).Returns(_eventSelection);
_outputSelectionSnapshot = new OutputSelections();
A.CallTo(() => _outputSelectionMapper.MapToSnapshot(_individualSimulation.OutputSelections)).Returns(_outputSelectionSnapshot);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotInteraction, _inductionProcess)).Returns(_intereactionSelection);
return(_completed);
}
public ParameterIdentificationAnalysisCreator(IChartFactory chartFactory, IOSPSuiteExecutionContext context, IContainerTask containerTask, IIdGenerator idGenerator, IObjectIdResetter objectIdResetter) : base(containerTask, context, objectIdResetter, idGenerator)
{
_chartFactory = chartFactory;
}
public IndividualScalingTask(IScalingMethodTask scalingMethodTask, IContainerTask containerTask)
{
_scalingMethodTask = scalingMethodTask;
_containerTask = containerTask;
}
public SensitivityAnalysisPKParameterAnalysisCreator(IContainerTask containerTask, IOSPSuiteExecutionContext executionContext, IObjectIdResetter objectIdResetter, IIdGenerator idGenerator)
: base(containerTask, executionContext, objectIdResetter, idGenerator)
{
}
protected override void Context()
{
sut = IoC.Resolve <ISerializationManager>();
_containerTask = IoC.Resolve <IContainerTask>();
}
public NameCorrector(IDialogCreator dialogCreator, IObjectTypeResolver objectTypeResolver, IContainerTask containerTask)
{
_dialogCreator = dialogCreator;
_objectTypeResolver = objectTypeResolver;
_containerTask = containerTask;
}
public IndividualExtractor(IExecutionContext executionContext, IEntityPathResolver entityPathResolver, IIndividualTask individualTask, IContainerTask containerTask, IBuildingBlockRepository buildingBlockRepository)
{
_executionContext = executionContext;
_entityPathResolver = entityPathResolver;
_individualTask = individualTask;
_containerTask = containerTask;
_buildingBlockRepository = buildingBlockRepository;
}
