public Converter521To522(IDefaultIndividualRetriever defaultIndividualRetriever, ICloner cloner, IRenalAgingCalculationMethodUpdater renalAgingCalculationMethodUpdater)
{
_defaultIndividualRetriever = defaultIndividualRetriever;
_cloner = cloner;
_renalAgingCalculationMethodUpdater = renalAgingCalculationMethodUpdater;
_defaultCache = new Cache <Species, Individual>(x => x.Species, x => null);
}
public Converter521To522(IDefaultIndividualRetriever defaultIndividualRetriever, ICloner cloner, IIndividualCalculationMethodsUpdater individualCalculationMethodsUpdater)
{
_defaultIndividualRetriever = defaultIndividualRetriever;
_cloner = cloner;
_individualCalculationMethodsUpdater = individualCalculationMethodsUpdater;
_defaultCache = new Cache <Species, Individual>(x => x.Species, x => null);
}
public Converter710To720(IDefaultIndividualRetriever defaultIndividualRetriever, ICloner cloner, IEntityPathResolver entityPathResolver, IOrganTypeRepository organTypeRepository, IIndividualCalculationMethodsUpdater individualCalculationMethodsUpdater)
{
_defaultIndividualRetriever = defaultIndividualRetriever;
_cloner = cloner;
_entityPathResolver = entityPathResolver;
_organTypeRepository = organTypeRepository;
_individualCalculationMethodsUpdater = individualCalculationMethodsUpdater;
}
public VSSCalculator(IDefaultIndividualRetriever defaultIndividualRetriever, ISpeciesRepository speciesRepository,
ISimulationFactory simulationFactory, IParameterFactory parameterFactory, IProtocolFactory protocolFactory)
{
_defaultIndividualRetriever = defaultIndividualRetriever;
_speciesRepository = speciesRepository;
_simulationFactory = simulationFactory;
_parameterFactory = parameterFactory;
_protocolFactory = protocolFactory;
}
public SnapshotObjectCreator(
IDefaultIndividualRetriever defaultIndividualRetriever,
IndividualMapper individualMapper,
ProjectMapper projectMapper
)
{
_defaultIndividualRetriever = defaultIndividualRetriever;
_individualMapper = individualMapper;
_projectMapper = projectMapper;
}
public Converter551To552(IDefaultIndividualRetriever defaultIndividualRetriever, ICloner cloner,
IEntityPathResolver entityPathResolver, IRenalAgingCalculationMethodUpdater renalAgingCalculationMethodUpdater,
IIndividualUpdater individualUpdater)
{
_defaultIndividualRetriever = defaultIndividualRetriever;
_cloner = cloner;
_entityPathResolver = entityPathResolver;
_renalAgingCalculationMethodUpdater = renalAgingCalculationMethodUpdater;
_individualUpdater = individualUpdater;
_defaultCache = new Cache <Species, Individual>(x => x.Species, x => null);
}
public GeneratePKMLTemplatesCommand(ISimulationMapper simulationMapper, IDefaultIndividualRetriever defaultIndividualRetriever,
IBuildConfigurationTask buildConfigurationTask, IPKMLPersistor pkmlPersistor, IDialogCreator dialogCreator,
IHeavyWorkManager heavyWorkManager, IMoBiExportTask moBiExportTask)
{
_simulationMapper = simulationMapper;
_defaultIndividualRetriever = defaultIndividualRetriever;
_buildConfigurationTask = buildConfigurationTask;
_pkmlPersistor = pkmlPersistor;
_dialogCreator = dialogCreator;
_heavyWorkManager = heavyWorkManager;
_moBiExportTask = moBiExportTask;
}
public Converter9To10(
IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver,
IDefaultIndividualRetriever defaultIndividualRetriever,
IMoleculeExpressionTask <Individual> moleculeExpressionTask,
ICloner cloner,
Converter90To100 coreConverter90To100
)
{
_individualMoleculeFactoryResolver = individualMoleculeFactoryResolver;
_defaultIndividualRetriever = defaultIndividualRetriever;
_moleculeExpressionTask = moleculeExpressionTask;
_cloner = cloner;
_coreConverter90To100 = coreConverter90To100;
}
public ImportObservedDataTask(IDataImporter dataImporter, IExecutionContext executionContext,
IDimensionRepository dimensionRepository, IBuildingBlockRepository buildingBlockRepository, ISpeciesRepository speciesRepository,
IDefaultIndividualRetriever defaultIndividualRetriever, IRepresentationInfoRepository representationInfoRepository,
IObservedDataTask observedDataTask, IParameterChangeUpdater parameterChangeUpdater)
{
_dataImporter = dataImporter;
_executionContext = executionContext;
_dimensionRepository = dimensionRepository;
_buildingBlockRepository = buildingBlockRepository;
_speciesRepository = speciesRepository;
_defaultIndividualRetriever = defaultIndividualRetriever;
_representationInfoRepository = representationInfoRepository;
_observedDataTask = observedDataTask;
_parameterChangeUpdater = parameterChangeUpdater;
}
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;
}
protected override void Context()
{
_speciesRepository = A.Fake <ISpeciesRepository>();
_view = A.Fake <IIndividualSettingsView>();
_defaultValueUpdater = A.Fake <IIndividualDefaultValueUpdater>();
_individualSettingsDTOMapper = A.Fake <IIndividualToIIndividualSettingsDTOMapper>();
_individualMapper = A.Fake <IIndividualSettingsDTOToIndividualMapper>();
_calculationMethodRepository = A.Fake <ICalculationMethodCategoryRepository>();
_subPopulation = A.Fake <IEnumerable <CategoryParameterValueVersionDTO> >();
_editValueOriginPresenter = A.Fake <IEditValueOriginPresenter>();
_defaultIndividualRetriever = A.Fake <IDefaultIndividualRetriever>();
_diseaseStateRepository = A.Fake <IDiseaseStateRepository>();
_individualSettingsDTO = new IndividualSettingsDTO();
_individualPropertiesDTO = new ObjectBaseDTO();
_speciesPopulation = A.Fake <SpeciesPopulation>();
_species = A.Fake <Species>();
_gender = A.Fake <Gender>();
_cmCat1 = new CalculationMethodCategory();
_cmCat2 = new CalculationMethodCategory();
_cmCat1.Add(new CalculationMethod());
_cmCat2.Add(new CalculationMethod());
_individualSettingsDTO.Species = _species;
_individualSettingsDTO.Population = _speciesPopulation;
_individualSettingsDTO.Gender = _gender;
A.CallTo(() => _defaultIndividualRetriever.DefaultIndividual()).Returns(_defaultIndividual);
A.CallTo(() => _individualSettingsDTOMapper.MapFrom(_defaultIndividual)).Returns(_individualSettingsDTO);
A.CallTo(() => _calculationMethodRepository.All()).Returns(new[] { _cmCat1, _cmCat2 });
_individualSettingsDTO.SubPopulation = _subPopulation;
_parentPresenter = A.Fake <IIndividualPresenter>();
sut = new IndividualSettingsPresenter(
_view,
_speciesRepository,
_calculationMethodRepository,
_defaultIndividualRetriever,
_defaultValueUpdater,
_individualSettingsDTOMapper,
_individualMapper,
_editValueOriginPresenter,
_diseaseStateRepository);
sut.InitializeWith(_parentPresenter);
}
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);
}
protected override void Context()
{
_executionContext = A.Fake <IExecutionContext>();
_compoundProcess = new EnzymaticProcessWithSpecies {
InternalName = "CompoundProcess"
};
_species = new Species {
Name = "NEW_SPECIES"
};
_compoundProcess.Species = new Species {
Name = "OLD_SPECIES"
};
sut = new SetSpeciesInCompoundProcessCommand(_compoundProcess, _species);
_defaultIndividualRetriever = A.Fake <IDefaultIndividualRetriever>();
A.CallTo(() => _executionContext.Resolve <IDefaultIndividualRetriever>()).Returns(_defaultIndividualRetriever);
_parameterMappingRepository = A.Fake <ICompoundProcessParameterMappingRepository>();
A.CallTo(() => _executionContext.Resolve <ICompoundProcessParameterMappingRepository>()).Returns(_parameterMappingRepository);
_individualParameter = DomainHelperForSpecs.ConstantParameterWithValue(value: 25).WithName("Matching");
_individualParameter.ValueOrigin.Method = ValueOriginDeterminationMethods.Assumption;
_individualParameter.ValueOrigin.Source = ValueOriginSources.ParameterIdentification;
_organism = new Organism {
_individualParameter
};
_individual = new Individual {
Root = new RootContainer {
_organism
}
};
A.CallTo(() => _defaultIndividualRetriever.DefaultIndividualFor(_species)).Returns(_individual);
_matchingIndividualParameter = DomainHelperForSpecs.ConstantParameterWithValue(isDefault: true).WithName("Matching");
_nonMatchingIndividualParameter = DomainHelperForSpecs.ConstantParameterWithValue(isDefault: true).WithName("NonMatching");
_compoundProcess.Add(_matchingIndividualParameter);
_compoundProcess.Add(_nonMatchingIndividualParameter);
_objectPath = new ObjectPath(_organism.Name, _individualParameter.Name);
A.CallTo(() => _parameterMappingRepository.HasMappedParameterFor(_compoundProcess.InternalName, _matchingIndividualParameter.Name)).Returns(true);
A.CallTo(() => _parameterMappingRepository.MappedParameterPathFor(_compoundProcess.InternalName, _matchingIndividualParameter.Name)).Returns(_objectPath);
}
public ImportObservedDataTask(IDataImporter dataImporter, IExecutionContext executionContext,
IDimensionRepository dimensionRepository, IBuildingBlockRepository buildingBlockRepository, ISpeciesRepository speciesRepository,
IDefaultIndividualRetriever defaultIndividualRetriever, IRepresentationInfoRepository representationInfoRepository,
IObservedDataTask observedDataTask, IParameterChangeUpdater parameterChangeUpdater, IDialogCreator dialogCreator, IContainer container,
IOSPSuiteXmlSerializerRepository modelingXmlSerializerRepository, IEventPublisher eventPublisher)
{
_dataImporter = dataImporter;
_executionContext = executionContext;
_dimensionRepository = dimensionRepository;
_buildingBlockRepository = buildingBlockRepository;
_speciesRepository = speciesRepository;
_defaultIndividualRetriever = defaultIndividualRetriever;
_representationInfoRepository = representationInfoRepository;
_observedDataTask = observedDataTask;
_parameterChangeUpdater = parameterChangeUpdater;
_dialogCreator = dialogCreator;
_container = container;
_modelingXmlSerializerRepository = modelingXmlSerializerRepository;
_eventPublisher = eventPublisher;
}
public Converter10to11(
IExpressionProfileFactory expressionProfileFactory,
IExpressionProfileUpdater expressionProfileUpdater,
IPKSimProjectRetriever projectRetriever,
IEventPublisher eventPublisher,
IRegistrationTask registrationTask,
IDefaultIndividualRetriever defaultIndividualRetriever,
ICloner cloner,
IContainerTask containerTask,
Converter100To110 coreConverter
)
{
_expressionProfileFactory = expressionProfileFactory;
_expressionProfileUpdater = expressionProfileUpdater;
_projectRetriever = projectRetriever;
_eventPublisher = eventPublisher;
_registrationTask = registrationTask;
_defaultIndividualRetriever = defaultIndividualRetriever;
_cloner = cloner;
_containerTask = containerTask;
_coreConverter = coreConverter;
}
public IndividualSettingsPresenter(
IIndividualSettingsView view,
ISpeciesRepository speciesRepository,
ICalculationMethodCategoryRepository calculationMethodCategoryRepository,
IDefaultIndividualRetriever defaultIndividualRetriever,
IIndividualDefaultValueUpdater defaultValueUpdater,
IIndividualToIIndividualSettingsDTOMapper individualSettingsDTOMapper,
IIndividualSettingsDTOToIndividualMapper individualMapper,
IEditValueOriginPresenter editValueOriginPresenter,
IDiseaseStateRepository diseaseStateRepository) : base(view)
{
_speciesRepository = speciesRepository;
_calculationMethodCategoryRepository = calculationMethodCategoryRepository;
_defaultIndividualRetriever = defaultIndividualRetriever;
_defaultValueUpdater = defaultValueUpdater;
_individualSettingsDTOMapper = individualSettingsDTOMapper;
_individualMapper = individualMapper;
_editValueOriginPresenter = editValueOriginPresenter;
_diseaseStateRepository = diseaseStateRepository;
_editValueOriginPresenter.ShowCaption = false;
AddSubPresenters(_editValueOriginPresenter);
_view.AddValueOriginView(_editValueOriginPresenter.View);
_editValueOriginPresenter.ValueOriginUpdated = valueOriginUpdated;
}
public override void GlobalContext()
{
base.GlobalContext();
_speciesRepository = IoC.Resolve <ISpeciesRepository>();
_individualRetriever = IoC.Resolve <IDefaultIndividualRetriever>();
}
