public override void GlobalContext()
{
base.GlobalContext();
_transporterContainerTemplateRepository = IoC.Resolve <ITransporterContainerTemplateRepository>();
var allTransporters = _transporterContainerTemplateRepository.TransportersFor(_individual.Species.Name, CoreConstants.Organ.Brain);
var influxBBB = allTransporters.Where(x => x.MembraneLocation == MembraneLocation.BloodBrainBarrier)
.FirstOrDefault(x => x.TransportType == TransportType.Influx);
_transporter = _transporterFactory.CreateFor(_individual).DowncastTo <IndividualTransporter>().WithName("TRANS");
var transportContainer = _transporter.ExpressionContainer(CoreConstants.Organ.Brain).DowncastTo <TransporterExpressionContainer>();
transportContainer.UpdatePropertiesFrom(influxBBB);
_individual.AddMolecule(_transporter);
_transportProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.ACTIVE_TRANSPORT_SPECIFIC_MM)
.DowncastTo <PartialProcess>());
_transportProcess.Name = "My Transport Process";
_compound.AddProcess(_transportProcess);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.TransportAndExcretionSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
CompoundName = _compound.Name, ProcessName = _transportProcess.Name, MoleculeName = _transporter.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
protected override void Context()
{
_expressionParameterMapper = A.Fake <IExpressionParameterMapper <TransporterExpressionParameterDTO> >();
_transporterContainerTemplateRepository = A.Fake <ITransporterContainerTemplateRepository>();
_transporterDirectionRepository = A.Fake <ITransportDirectionRepository>();
sut = new IndividualTransporterToTransporterExpressionDTOMapper(_expressionParameterMapper, _transporterDirectionRepository, _transporterContainerTemplateRepository);
}
public TransportContainerUpdater(
ITransporterContainerTemplateRepository transporterContainerTemplateRepository,
IEventPublisher eventPublisher)
{
_transporterContainerTemplateRepository = transporterContainerTemplateRepository;
_eventPublisher = eventPublisher;
}
protected override void Context()
{
_view = A.Fake <IIndividualTransporterExpressionsView>();
_parameterTask = A.Fake <IEditParameterPresenterTask>();
_moleculeTask = A.Fake <IMoleculeExpressionTask <Individual> >();
_transporterMapper = A.Fake <IIndividualTransporterToTransporterExpressionDTOMapper>();
_transportRepository = A.Fake <ITransporterContainerTemplateRepository>();
_moleculePropertiesPresenter = A.Fake <IIndividualMoleculePropertiesPresenter <Individual> >();
sut = new IndividualTransporterExpressionsPresenter <Individual>(_view, _parameterTask, _moleculeTask, _transporterMapper, _transportRepository, _moleculePropertiesPresenter);
}
public IndividualTransporterToTransporterExpressionDTOMapper(
IExpressionParameterMapper <TransporterExpressionParameterDTO> expressionParameterMapper,
ITransportDirectionRepository transportDirectionRepository,
ITransporterContainerTemplateRepository transporterContainerTemplateRepository
)
{
_expressionParameterMapper = expressionParameterMapper;
_transportDirectionRepository = transportDirectionRepository;
_transporterContainerTemplateRepository = transporterContainerTemplateRepository;
}
public UsedMoleculeRepository(
IPKSimProjectRetriever projectRetriever,
IOntogenyRepository ontogenyRepository,
IMoleculeParameterRepository moleculeParameterRepository,
ITransporterContainerTemplateRepository transporterContainerTemplateRepository)
{
_projectRetriever = projectRetriever;
_ontogenyRepository = ontogenyRepository;
_moleculeParameterRepository = moleculeParameterRepository;
_transporterContainerTemplateRepository = transporterContainerTemplateRepository;
}
public IndividualTransporterExpressionsPresenter(IIndividualTransporterExpressionsView view, IEditParameterPresenterTask parameterTask, IMoleculeExpressionTask <TSimulationSubject> moleculeExpressionTask,
IIndividualTransporterToTransporterExpressionDTOMapper transporterExpressionDTOMapper,
ITransporterContainerTemplateRepository transporterContainerTemplateRepository, IIndividualMoleculePropertiesPresenter <TSimulationSubject> moleculePropertiesPresenter)
: base(view, parameterTask)
{
_moleculeExpressionTask = moleculeExpressionTask;
_transporterExpressionDTOMapper = transporterExpressionDTOMapper;
_moleculePropertiesPresenter = moleculePropertiesPresenter;
_transporterContainerTemplateRepository = transporterContainerTemplateRepository;
AddSubPresenters(_moleculePropertiesPresenter);
view.AddMoleculePropertiesView(_moleculePropertiesPresenter.View);
}
protected override void Context()
{
_project = new PKSimProject();
_projectRetriever = A.Fake <IPKSimProjectRetriever>();
_transporterContainerTemplateRepository = A.Fake <ITransporterContainerTemplateRepository>();
A.CallTo(() => _projectRetriever.Current).Returns(_project);
_compound1 = A.Fake <Compound>();
_compound1.IsLoaded = false;
_compound2 = new Compound {
IsLoaded = true
};
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "ProjA", Name = "P1"
});
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "ProjC", Name = "P2"
});
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "ProjB", Name = "P3"
});
_ontogenyRepository = A.Fake <IOntogenyRepository>();
_moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>();
_expressionProfile = A.Fake <ExpressionProfile>();
_expressionProfile.IsLoaded = true;
A.CallTo(() => _expressionProfile.MoleculeName).Returns("ProjE");
_project.AddBuildingBlock(_compound1);
_project.AddBuildingBlock(_compound2);
_project.AddBuildingBlock(_expressionProfile);
sut = new UsedMoleculeRepository(_projectRetriever, _ontogenyRepository, _moleculeParameterRepository, _transporterContainerTemplateRepository);
var molParam1 = new MoleculeParameter {
MoleculeName = "DbB"
};
var molParam2 = new MoleculeParameter {
MoleculeName = "DbA"
};
A.CallTo(() => _moleculeParameterRepository.All()).Returns(new[] { molParam1, molParam2 });
A.CallTo(() => _transporterContainerTemplateRepository.AllTransporterNames).Returns(new[] { "ATRANS1", "TRANS2" });
A.CallTo(() => _ontogenyRepository.AllFor(CoreConstants.Species.HUMAN)).Returns(new[] { new DatabaseOntogeny {
Name = "OntoC"
} });
}
protected override void Context()
{
_repository = A.Fake<ITransporterContainerTemplateRepository>();
_eventPublisher = A.Fake<IEventPublisher>();
sut = new TransportContainerUpdater(_repository, _eventPublisher);
}
protected override void Context()
{
_repository = A.Fake <ITransporterContainerTemplateRepository>();
_eventPublisher = A.Fake <IEventPublisher>();
_transportDirectionRepository = A.Fake <ITransportDirectionRepository>();
sut = new TransportContainerUpdater(_repository, _eventPublisher);
_fractionExpressedApical = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.FRACTION_EXPRESSED_APICAL);
_fractionExpressedApicalMucosa = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.FRACTION_EXPRESSED_APICAL);
_fractionExpressedApicalBone = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.FRACTION_EXPRESSED_APICAL);
//Indicates that this parameter should not be visible to the user and therefore remains unchanged
_fractionExpressedApicalBone.Visible = false;
_individual = A.Fake <ISimulationSubject>();
_individual.Species.Name = _species;
_transporter = new IndividualTransporter {
TransportType = TransportType.Efflux, Name = "toto"
};
var organism = new Organism();
var mucosa = new Container().WithName(CoreConstants.Compartment.MUCOSA).WithParentContainer(organism);
var liver = new Container().WithName(CoreConstants.Organ.LIVER).WithParentContainer(organism);
var liverCell = new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithParentContainer(liver);
var kidney = new Container().WithName(CoreConstants.Organ.KIDNEY).WithParentContainer(organism);
var kidneyCell = new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithParentContainer(kidney);
var bone = new Container().WithName(CoreConstants.Organ.BONE).WithParentContainer(organism);
var boneInterstitial = new Container().WithName(CoreConstants.Compartment.INTERSTITIAL).WithParentContainer(bone);
_transporterWithTemplate = new TransporterExpressionContainer {
TransportDirection = TransportDirectionId.InfluxInterstitialToIntracellular
}
.WithParentContainer(liverCell);
_transporterWithoutTemplate = new TransporterExpressionContainer
{
TransportDirection = TransportDirectionId.EffluxIntracellularToInterstitial
}
.WithParentContainer(kidneyCell);
_transporterInMucosa = new TransporterExpressionContainer {
TransportDirection = TransportDirectionId.InfluxInterstitialToIntracellular
}
.WithParentContainer(mucosa);
_transporterInBone = new TransporterExpressionContainer {
TransportDirection = TransportDirectionId.InfluxInterstitialToIntracellular
}
.WithParentContainer(boneInterstitial);
_transporterInMucosa.Add(_fractionExpressedApicalMucosa);
_transporterWithoutTemplate.Add(_fractionExpressedApical);
_transporterInBone.Add(_fractionExpressedApicalBone);
A.CallTo(() => _individual.AllMoleculeContainersFor <TransporterExpressionContainer>(_transporter))
.Returns(new[] { _transporterWithTemplate, _transporterWithoutTemplate, _transporterInMucosa, _transporterInBone });
_transporterContainerTemplate = new TransporterContainerTemplate {
TransportType = TransportType.Influx
};
_allTransporterTemplates.Add(_transporterContainerTemplate);
A.CallTo(() => _repository.HasTransporterTemplateFor(_species, _transporter.Name)).Returns(true);
A.CallTo(() => _repository.TransportTypeFor(_species, _transporter.Name)).Returns(TransportType.Influx);
A.CallTo(() => _repository.TransportersFor(_species, liver.Name, _transporter.Name)).Returns(_allTransporterTemplates);
A.CallTo(() => _repository.TransportersFor(_species, kidney.Name, _transporter.Name)).Returns(new List <TransporterContainerTemplate>());
}
public IndividualTransporterFactory(IObjectBaseFactory objectBaseFactory, IParameterFactory parameterFactory,
IObjectPathFactory objectPathFactory, IEntityPathResolver entityPathResolver,
ITransporterContainerTemplateRepository transporterContainerTemplateRepository) : base(objectBaseFactory, parameterFactory, objectPathFactory, entityPathResolver)
{
_transporterContainerTemplateRepository = transporterContainerTemplateRepository;
}
