private bool areSame(TransporterContainerTemplate transporter1, TransporterContainerTemplate transporter2)
{
return
(transporter1.Gene == transporter2.Gene &&
transporter1.MembraneLocation == transporter2.MembraneLocation &&
transporter1.TransportType == transporter2.TransportType);
}
private void updateTransporterContainerFromTemplate(TransporterExpressionContainer expressionContainer,
TransporterContainerTemplate transporterContainerTemplate, TransportType defaultTransportType)
{
var transportType = transporterContainerTemplate?.TransportType ?? defaultTransportType;
expressionContainer.TransportDirection = TransportDirections.DefaultDirectionFor(transportType, expressionContainer);
}
protected override void Context()
{
base.Context();
_transporter = new IndividualTransporter {
TransportType = TransportType.Efflux, Name = "toto"
};
_transporterWithTemplate = new TransporterExpressionContainer {
MembraneLocation = MembraneLocation.Apical
}.WithName(_liver);
_transporterWithoutTemplate = new TransporterExpressionContainer {
MembraneLocation = MembraneLocation.Basolateral
}.WithName("Kidney");
_transporter.Add(_transporterWithTemplate);
_transporter.Add(_transporterWithoutTemplate);
_transporterContainerTemplate = new TransporterContainerTemplate {
MembraneLocation = MembraneLocation.Apical, TransportType = TransportType.Influx
};
_defaultTemplate = new TransporterContainerTemplate {
MembraneLocation = MembraneLocation.Basolateral, 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, _transporter.Name)).Returns(_allTransporterTemplates);
A.CallTo(() => _repository.TransportersFor(_species, _kidney, _transporter.Name)).Returns(new List <TransporterContainerTemplate>());
A.CallTo(() => _repository.TransportersFor(_species, _kidney)).Returns(new List <TransporterContainerTemplate> {
_defaultTemplate
});
}
protected override void Context()
{
base.Context();
_transporterContainer = A.Fake<ITransporterExpressionContainer>();
A.CallTo(() => _transporterContainer.Name).Returns(_liver);
_species = "human";
A.CallTo(() => _repository.TransportersFor(_species, _liver)).Returns(_allTransporters);
_membrane = MembraneLocation.Apical;
_transportType = TransportType.Efflux;
_transporterContainerTemplate = new TransporterContainerTemplate {MembraneLocation = _membrane, TransportType = _transportType};
_allTransporters.Add(_transporterContainerTemplate);
}
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>());
}
