protected override void Context()
{
_view = A.Fake <IExpressionProfileMoleculesView>();
_expressionProfileFactory = A.Fake <IExpressionProfileFactory>();
_applicationController = A.Fake <IApplicationController>();
_mapper = A.Fake <IExpressionProfileToExpressionProfileDTOMapper>();
_enzymePresenter = A.Fake <IIndividualEnzymeExpressionsPresenter <Individual> >();
_expressionProfileUpdater = A.Fake <IExpressionProfileUpdater>();
_expressionProfileProteinDatabaseTask = A.Fake <IExpressionProfileProteinDatabaseTask>();
_moleculeParameterTask = A.Fake <IMoleculeParameterTask>();
sut = new ExpressionProfileMoleculesPresenter(
_view,
_expressionProfileFactory,
_applicationController,
_mapper,
_expressionProfileProteinDatabaseTask,
_expressionProfileUpdater,
_moleculeParameterTask);
sut.InitializeWith(new PKSimMacroCommand());
_expressionProfile = A.Fake <ExpressionProfile>();
_expressionProfileDTO = new ExpressionProfileDTO();
_enzyme = new IndividualEnzyme();
A.CallTo(() => _expressionProfile.Molecule).Returns(_enzyme);
A.CallTo(() => _mapper.MapFrom(_expressionProfile)).Returns(_expressionProfileDTO);
A.CallTo(() => _applicationController.Start <IIndividualEnzymeExpressionsPresenter <Individual> >()).Returns(_enzymePresenter);
}
public RenameBuildingBlockTask(
IBuildingBlockTask buildingBlockTask,
IBuildingBlockInProjectManager buildingBlockInProjectManager,
IApplicationController applicationController,
ILazyLoadTask lazyLoadTask, IContainerTask containerTask,
IHeavyWorkManager heavyWorkManager,
IRenameAbsolutePathVisitor renameAbsolutePathVisitor,
IObjectReferencingRetriever objectReferencingRetriever,
IProjectRetriever projectRetriever,
IParameterIdentificationSimulationPathUpdater simulationPathUpdater,
IDataRepositoryNamer dataRepositoryNamer,
ICurveNamer curveNamer,
IExpressionProfileUpdater expressionProfileUpdater)
{
_buildingBlockTask = buildingBlockTask;
_buildingBlockInProjectManager = buildingBlockInProjectManager;
_applicationController = applicationController;
_lazyLoadTask = lazyLoadTask;
_containerTask = containerTask;
_heavyWorkManager = heavyWorkManager;
_renameAbsolutePathVisitor = renameAbsolutePathVisitor;
_objectReferencingRetriever = objectReferencingRetriever;
_projectRetriever = projectRetriever;
_simulationPathUpdater = simulationPathUpdater;
_dataRepositoryNamer = dataRepositoryNamer;
_curveNamer = curveNamer;
_expressionProfileUpdater = expressionProfileUpdater;
}
protected override void Context()
{
_view = A.Fake <ICreateExpressionProfileView>();
_mapper = A.Fake <IExpressionProfileToExpressionProfileDTOMapper>();
_expressionProfileUpdater = A.Fake <IExpressionProfileUpdater>();
_expressionProfileFactory = A.Fake <IExpressionProfileFactory>();
_dialogCreator = A.Fake <IDialogCreator>();
sut = new CloneExpressionProfilePresenter(_view, _mapper, _expressionProfileUpdater, _expressionProfileFactory, _dialogCreator);
}
public MoleculeExpressionTask(IExecutionContext executionContext,
IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver,
ISimulationSubjectExpressionTask <TSimulationSubject> simulationSubjectExpressionTask,
IExpressionProfileUpdater expressionProfileUpdater)
{
_executionContext = executionContext;
_individualMoleculeFactoryResolver = individualMoleculeFactoryResolver;
_simulationSubjectExpressionTask = simulationSubjectExpressionTask;
_expressionProfileUpdater = expressionProfileUpdater;
}
public SimulationParametersToBuildingBlockUpdater(
IContainerTask containerTask,
IParameterSetUpdater parameterSetUpdater,
IExpressionProfileUpdater expressionProfileUpdater,
IExecutionContext executionContext)
{
_containerTask = containerTask;
_parameterSetUpdater = parameterSetUpdater;
_expressionProfileUpdater = expressionProfileUpdater;
_executionContext = executionContext;
}
public CloneExpressionProfilePresenter(
ICreateExpressionProfileView view,
IExpressionProfileToExpressionProfileDTOMapper expressionProfileDTOMapper,
IExpressionProfileUpdater expressionProfileUpdater,
IExpressionProfileFactory expressionProfileFactory,
IDialogCreator dialogCreator) : base(view)
{
_expressionProfileDTOMapper = expressionProfileDTOMapper;
_expressionProfileUpdater = expressionProfileUpdater;
_expressionProfileFactory = expressionProfileFactory;
_dialogCreator = dialogCreator;
}
public ExpressionProfileMoleculesPresenter(
IExpressionProfileMoleculesView view,
IExpressionProfileFactory expressionProfileFactory,
IApplicationController applicationController,
IExpressionProfileToExpressionProfileDTOMapper expressionProfileDTOMapper,
IExpressionProfileProteinDatabaseTask expressionProfileProteinDatabaseTask,
IExpressionProfileUpdater expressionProfileUpdater,
IMoleculeParameterTask moleculeParameterTask) : base(view)
{
_expressionProfileFactory = expressionProfileFactory;
_applicationController = applicationController;
_expressionProfileDTOMapper = expressionProfileDTOMapper;
_expressionProfileProteinDatabaseTask = expressionProfileProteinDatabaseTask;
_expressionProfileUpdater = expressionProfileUpdater;
_moleculeParameterTask = moleculeParameterTask;
}
protected override void Context()
{
_individual = new Individual {
OriginData = new OriginData {
Species = new Species().WithName("Human")
}
};
_ontogeny = new DatabaseOntogeny {
Name = "toto"
};
_executionContext = A.Fake <IExecutionContext>();
_individualMoleculeFactoryResolver = A.Fake <IIndividualMoleculeFactoryResolver>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
var proteinFactory = A.Fake <IIndividualMoleculeFactory>();
_expressionProfileUpdater = A.Fake <IExpressionProfileUpdater>();
_moleculeContainer1 = new MoleculeExpressionContainer().WithName("C1");
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
_moleculeContainer2 = new MoleculeExpressionContainer().WithName("C2");
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
A.CallTo(() => _individualMoleculeFactoryResolver.FactoryFor <IndividualProtein>()).Returns(proteinFactory);
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
A.CallTo(() => proteinFactory.AddMoleculeTo(_individual, A <string> ._)).Returns(_molecule);
A.CallTo(() => _ontogenyRepository.AllFor(_individual.Species.Name)).Returns(new[] { _ontogeny, new DatabaseOntogeny {
Name = "tralala"
}, });
A.CallTo(() => _executionContext.Resolve <IOntogenyRepository>()).Returns(_ontogenyRepository);
_subjectExpressionTask = new IndividualExpressionTask(_executionContext);
sut = new MoleculeExpressionTask <Individual>(
_executionContext,
_individualMoleculeFactoryResolver,
_subjectExpressionTask,
_expressionProfileUpdater
);
}
protected override void Context()
{
_applicationController = A.Fake <IApplicationController>();
_buildingBlockTask = A.Fake <IBuildingBlockTask>();
_buildingBlockInProjectManager = A.Fake <IBuildingBlockInProjectManager>();
_lazyloadTask = A.Fake <ILazyLoadTask>();
_heavyWorkManager = A.Fake <IHeavyWorkManager>();
_containerTask = A.Fake <IContainerTask>();
_objectReferencingRetriever = A.Fake <IObjectReferencingRetriever>();
_projectRetriever = A.Fake <IProjectRetriever>();
_renameAbsolutePathVisitor = new RenameAbsolutePathVisitor();
_objectPathFactory = new ObjectPathFactoryForSpecs();
_parameterIdentificationSimulationPathUpdater = A.Fake <IParameterIdentificationSimulationPathUpdater>();
_dataRepositoryNamer = A.Fake <IDataRepositoryNamer>();
_curveNamer = A.Fake <ICurveNamer>();
_expressionProfileUpdater = A.Fake <IExpressionProfileUpdater>();
sut = new RenameBuildingBlockTask(
_buildingBlockTask,
_buildingBlockInProjectManager,
_applicationController,
_lazyloadTask,
_containerTask,
_heavyWorkManager,
_renameAbsolutePathVisitor,
_objectReferencingRetriever,
_projectRetriever,
_parameterIdentificationSimulationPathUpdater,
_dataRepositoryNamer,
_curveNamer,
_expressionProfileUpdater);
_initialSimulationName = "S";
_individualSimulation = new IndividualSimulation().WithName(_initialSimulationName);
_individualSimulation.Model = new Model().WithName(_initialSimulationName);
_simulation = _individualSimulation;
_root = new Container().WithName(_initialSimulationName);
_individualSimulation.Model.Root = _root;
}
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;
}
