protected override void Context()
{
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <Individual> >();
_querySettingsMapper = A.Fake <IMoleculeToQueryExpressionSettingsMapper>();
_geneExpressionsDatabasePathManager = A.Fake <IGeneExpressionsDatabasePathManager>();
_applicationController = A.Fake <IApplicationController>();
sut = new EditMoleculeTask <Individual>(_moleculeExpressionTask, _applicationController);
_expressionProfileSelectionPresenter = A.Fake <IExpressionProfileSelectionPresenter>();
A.CallTo(() => _applicationController.Start <IExpressionProfileSelectionPresenter>()).Returns(_expressionProfileSelectionPresenter);
_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));
_individual = new Individual {
OriginData = new OriginData {
Species = new Species {
Name = "Human", DisplayName = "Human"
}
}
};
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
}
public ExpressionProfileProteinDatabaseTask(
IGeneExpressionsDatabasePathManager geneExpressionsDatabasePathManager,
IApplicationController applicationController,
IMoleculeToQueryExpressionSettingsMapper queryExpressionSettingsMapper,
IMoleculeExpressionTask <Individual> moleculeExpressionTask)
{
_geneExpressionsDatabasePathManager = geneExpressionsDatabasePathManager;
_applicationController = applicationController;
_queryExpressionSettingsMapper = queryExpressionSettingsMapper;
_moleculeExpressionTask = moleculeExpressionTask;
}
protected override void Context()
{
_individual = new Individual();
_individual.OriginData = new OriginData();
_individual.OriginData.Species = new Species().WithName("Human");
_ontogeny = new DatabaseOntogeny {
Name = "toto"
};
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_executionContext = A.Fake <IExecutionContext>();
_proteinExpressionPresenter = A.Fake <IProteinExpressionsPresenter>();
_simpleMoleculePresenter = A.Fake <ISimpleMoleculePresenter>();
_querySettingsMapper = A.Fake <IMoleculeToQueryExpressionSettingsMapper>();
_applicationController = A.Fake <IApplicationController>();
_individualMoleculeFactoryResolver = A.Fake <IIndividualMoleculeFactoryResolver>();
_transportContainerUpdater = A.Fake <ITransportContainerUpdater>();
_containerTask = A.Fake <IContainerTask>();
_moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>();
_proteinExpressionDbPathManager = A.Fake <IProteinExpressionsDatabasePathManager>();
A.CallTo(() => _applicationController.Start <IProteinExpressionsPresenter>()).Returns(_proteinExpressionPresenter);
A.CallTo(() => _applicationController.Start <ISimpleMoleculePresenter>()).Returns(_simpleMoleculePresenter);
_ontogenyRepository = A.Fake <IOntogenyRepository>();
var proteinFactory = A.Fake <IIndividualMoleculeFactory>();
_moleculeContainer1 = new MoleculeExpressionContainer().WithName("C1");
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameter.RelExp));
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameter.RelExpNorm));
_moleculeContainer2 = new MoleculeExpressionContainer().WithName("C2");
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameter.RelExp));
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameter.RelExpNorm));
A.CallTo(() => _individualMoleculeFactoryResolver.FactoryFor <IndividualProtein>()).Returns(proteinFactory);
A.CallTo(() => proteinFactory.CreateFor(_individual)).Returns(_molecule);
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(CoreConstants.Parameter.REFERENCE_CONCENTRATION));
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(20).WithName(CoreConstants.Parameter.HALF_LIFE_LIVER));
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(30).WithName(CoreConstants.Parameter.HALF_LIFE_INTESTINE));
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);
_ontogenyTask = A.Fake <IOntogenyTask <Individual> >();
sut = new MoleculeExpressionTask <Individual>(_applicationController, _executionContext,
_individualMoleculeFactoryResolver, _querySettingsMapper,
_containerTask, _proteinExpressionDbPathManager,
_ontogenyRepository, _transportContainerUpdater, _moleculeParameterRepository, _subjectExpressionTask, _ontogenyTask);
}
protected override void Context()
{
_geneExpressionDatabasePathManager = A.Fake <IGeneExpressionsDatabasePathManager>();
_applicationController = A.Fake <IApplicationController>();
_querySettingsMapper = A.Fake <IMoleculeToQueryExpressionSettingsMapper>();
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <Individual> >();
sut = new ExpressionProfileProteinDatabaseTask(_geneExpressionDatabasePathManager, _applicationController, _querySettingsMapper, _moleculeExpressionTask);
_proteinExpressionPresenter = A.Fake <IProteinExpressionsPresenter>();
A.CallTo(() => _applicationController.Start <IProteinExpressionsPresenter>()).Returns(_proteinExpressionPresenter);
}
public MoleculeExpressionTask(IApplicationController applicationController, IExecutionContext executionContext,
IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver,
IMoleculeToQueryExpressionSettingsMapper queryExpressionSettingsMapper,
IContainerTask containerTask,
IProteinExpressionsDatabasePathManager proteinExpressionsDatabasePathManager,
IOntogenyRepository ontogenyRepository,
ITransportContainerUpdater transportContainerUpdater,
ISimulationSubjectExpressionTask <TSimulationSubject> simulationSubjectExpressionTask,
IOntogenyTask <TSimulationSubject> ontogenyTask,
IMoleculeParameterTask moleculeParameterTask)
{
_applicationController = applicationController;
_executionContext = executionContext;
_individualMoleculeFactoryResolver = individualMoleculeFactoryResolver;
_queryExpressionSettingsMapper = queryExpressionSettingsMapper;
_containerTask = containerTask;
_proteinExpressionsDatabasePathManager = proteinExpressionsDatabasePathManager;
_ontogenyRepository = ontogenyRepository;
_transportContainerUpdater = transportContainerUpdater;
_simulationSubjectExpressionTask = simulationSubjectExpressionTask;
_ontogenyTask = ontogenyTask;
_moleculeParameterTask = moleculeParameterTask;
}
