public ExpressionContainerMapper(
ParameterMapper parameterMapper,
ITransportContainerUpdater transportContainerUpdater,
ILogger logger)
{
_parameterMapper = parameterMapper;
_transportContainerUpdater = transportContainerUpdater;
_logger = logger;
}
public MoleculeParameterTask(
IMoleculeParameterRepository moleculeParameterRepository,
ITransportContainerUpdater transportContainerUpdater,
IOntogenyRepository ontogenyRepository,
IOntogenyTask ontogenyTask)
{
_moleculeParameterRepository = moleculeParameterRepository;
_transportContainerUpdater = transportContainerUpdater;
_ontogenyRepository = ontogenyRepository;
_ontogenyTask = ontogenyTask;
}
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()
{
_transportContainerUpdater = A.Fake <ITransportContainerUpdater>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
_ontogenyTask = A.Fake <IOntogenyTask>();
_moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>();
sut = new MoleculeParameterTask(_moleculeParameterRepository, _transportContainerUpdater, _ontogenyRepository, _ontogenyTask);
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(CoreConstants.Parameters.REFERENCE_CONCENTRATION));
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(20).WithName(CoreConstants.Parameters.HALF_LIFE_LIVER));
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(30).WithName(CoreConstants.Parameters.HALF_LIFE_INTESTINE));
}
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;
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_transportContainerUpdater = A.Fake <ITransportContainerUpdater>();
_logger = A.Fake <ILogger>();
sut = new ExpressionContainerMapper(_parameterMapper, _transportContainerUpdater, _logger);
_relativeExpressionParameter = DomainHelperForSpecs.ConstantParameterWithValue(0, isDefault: true).WithName(CoreConstants.Parameters.REL_EXP);
_moleculeExpressionContainer = new MoleculeExpressionContainer().WithName("EXP");
_moleculeExpressionContainer.Add(_relativeExpressionParameter);
_transporterRelativeExpressionParameter = DomainHelperForSpecs.ConstantParameterWithValue(0, isDefault: true).WithName(CoreConstants.Parameters.REL_EXP);
_transporterExpressionContainer = new TransporterExpressionContainer().WithName("TRANS");
_transporterExpressionContainer.MembraneLocation = MembraneLocation.Apical;
_transporterExpressionContainer.Add(_transporterRelativeExpressionParameter);
_individual = new Individual {
OriginData = new Model.OriginData {
Species = new Species().WithName("Human")
}
};
_expressionContainerMapperContext = new ExpressionContainerMapperContext
{
SimulationSubject = _individual
};
_enzyme = new IndividualEnzyme {
_moleculeExpressionContainer
};
_transporter = new IndividualTransporter {
_transporterExpressionContainer
};
return(_completed);
}
