public void SetDefaultSettingsForTransporter(IndividualTransporter transporter, string species, string transporterName)
{
transporter.TransportType = _transporterContainerTemplateRepository.TransportTypeFor(species, transporterName);
foreach (var transporterContainer in transporter.AllExpressionsContainers())
{
//there is a db template
var tranporterTemplate = _transporterContainerTemplateRepository.TransportersFor(species, transporterContainer.Name, transporterName).FirstOrDefault();
if (tranporterTemplate != null)
{
transporterContainer.UpdatePropertiesFrom(tranporterTemplate);
}
else
{
UpdateTransporterFromTemplate(transporterContainer, species, MembraneLocationToUse(transporterContainer, transporter.TransportType), transporter.TransportType);
}
}
if (_transporterContainerTemplateRepository.HasTransporterTemplateFor(species, transporterName))
{
return;
}
//No template was found for the given name. Raise event warning
_eventPublisher.PublishEvent(new NoTranporterTemplateAvailableEvent(transporter));
}
public void UpdateExpressionParameters(IndividualTransporterDTO individualTransporterDTO, ISimulationSubject simulationSubject)
{
var transporter = individualTransporterDTO.Transporter;
individualTransporterDTO.ClearExpressionParameters();
//Local parameters
foreach (var transporterExpressionContainer in simulationSubject.AllMoleculeContainersFor <TransporterExpressionContainer>(transporter))
{
var organ = transporterExpressionContainer.LogicalContainer;
var isInOrganWithLumenOrBrain = organ.IsOrganWithLumen() || organ.IsBrain();
foreach (var parameter in transporterExpressionContainer.AllParameters())
{
var expressionParameterDTO = _expressionParameterMapper.MapFrom(parameter);
expressionParameterDTO.TransporterExpressionContainer = transporterExpressionContainer;
expressionParameterDTO.IsInOrganWithLumenOrBrain = isInOrganWithLumenOrBrain;
var direction = retrieveTransporterDirectionFor(transporterExpressionContainer, parameter, isInOrganWithLumenOrBrain);
expressionParameterDTO.TransportDirection = _transportDirectionRepository.ById(direction);
individualTransporterDTO.AddExpressionParameter(expressionParameterDTO);
}
}
//Global parameters;
foreach (var parameter in transporter.AllGlobalExpressionParameters)
{
var expressionParameter = _expressionParameterMapper.MapFrom(parameter);
expressionParameter.TransporterExpressionContainer = parameter.IsNamed(REL_EXP_BLOOD_CELLS)
? transporter.BloodCellsContainer
: transporter.VascularEndotheliumContainer;
var direction = expressionParameter.TransporterExpressionContainer.TransportDirection;
expressionParameter.TransportDirection = _transportDirectionRepository.ById(direction);
individualTransporterDTO.AddExpressionParameter(expressionParameter);
}
var hasTemplateForSpecies = _transporterContainerTemplateRepository.HasTransporterTemplateFor(simulationSubject.Species.Name, transporter.Name);
individualTransporterDTO.DefaultAvailableInDatabase = hasTemplateForSpecies;
}
public void SetDefaultSettingsForTransporter(ISimulationSubject simulationSubject, IndividualTransporter transporter, string transporterName)
{
var speciesName = simulationSubject.Species.Name;
transporter.TransportType = _transporterContainerTemplateRepository.TransportTypeFor(speciesName, transporterName);
foreach (var transporterContainer in simulationSubject.AllMoleculeContainersFor <TransporterExpressionContainer>(transporter))
{
//there is a db template
var transporterTemplate = _transporterContainerTemplateRepository
.TransportersFor(speciesName, transporterContainer.LogicalContainerName, transporterName)
.FirstOrDefault();
updateTransporterContainerFromTemplate(transporterContainer, transporterTemplate, transporter.TransportType);
}
if (_transporterContainerTemplateRepository.HasTransporterTemplateFor(speciesName, transporterName))
{
return;
}
//No template was found for the given name. Raise event warning
_eventPublisher.PublishEvent(new NoTransporterTemplateAvailableEvent(transporter));
}
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>());
}