private void updateTransporterContainerFromTemplate(TransporterExpressionContainer expressionContainer,
TransporterContainerTemplate transporterContainerTemplate, TransportType defaultTransportType)
{
var transportType = transporterContainerTemplate?.TransportType ?? defaultTransportType;
expressionContainer.TransportDirection = TransportDirections.DefaultDirectionFor(transportType, expressionContainer);
}
public void should_return_the_expected_direction_for_tissue()
{
_transporterExpressionContainer.WithParentContainer(_bone_cell);
TransportDirections.DefaultDirectionFor(TransportType.Influx, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.InfluxInterstitialToIntracellular);
TransportDirections.DefaultDirectionFor(TransportType.BiDirectional, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.BiDirectionalInterstitialIntracellular);
TransportDirections.DefaultDirectionFor(TransportType.Efflux, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.EffluxIntracellularToInterstitial);
}
public void should_return_the_expected_direction_for_liver_and_kidney()
{
_transporterExpressionContainer.WithParentContainer(_liver_cell);
_transporterExpressionContainer.TransportDirection = TransportDirectionId.ExcretionLiver;
TransportDirections.DefaultDirectionFor(TransportType.Influx, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.ExcretionLiver);
TransportDirections.DefaultDirectionFor(TransportType.Efflux, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.ExcretionLiver);
_transporterExpressionContainer.WithParentContainer(_kidney_cell);
_transporterExpressionContainer.TransportDirection = TransportDirectionId.ExcretionKidney;
TransportDirections.DefaultDirectionFor(TransportType.Influx, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.ExcretionKidney);
TransportDirections.DefaultDirectionFor(TransportType.Efflux, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.ExcretionKidney);
}
private void convertIndividualTransporter(IndividualMolecule moleculeToConvert, IndividualMolecule newMolecule, Individual individual)
{
var transporterToConvert = moleculeToConvert as IndividualTransporter;
var newTransporter = newMolecule as IndividualTransporter;
if (transporterToConvert == null || newTransporter == null)
{
return;
}
newTransporter.TransportType = transporterToConvert.TransportType;
var allTransporterExpressionContainers = individual.AllMoleculeContainersFor <TransporterExpressionContainer>(newTransporter)
.Where(x => x.TransportDirection != TransportDirectionId.None).ToList();
//Ensure we update the default direction based on the selected transporter type
allTransporterExpressionContainers.Each(x => x.TransportDirection = TransportDirections.DefaultDirectionFor(newTransporter.TransportType, x));
moleculeToConvert.GetAllChildren <TransporterExpressionContainer>().Each(x => convertTransportContainer(x, allTransporterExpressionContainers));
}
public void should_return_the_expected_direction_for_organ_with_lumen()
{
_transporterExpressionContainer.WithParentContainer(_mucosaDuodenumInt);
TransportDirections.DefaultDirectionFor(TransportType.Influx, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.InfluxInterstitialToIntracellular);
TransportDirections.DefaultDirectionFor(TransportType.BiDirectional, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.BiDirectionalInterstitialIntracellular);
TransportDirections.DefaultDirectionFor(TransportType.Efflux, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.EffluxIntracellularToInterstitial);
_transporterExpressionContainer.WithParentContainer(_mucosaDuodenumCell);
TransportDirections.DefaultDirectionFor(TransportType.Influx, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.InfluxLumenToMucosaIntracellular);
TransportDirections.DefaultDirectionFor(TransportType.BiDirectional, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.BiDirectionalLumenMucosaIntracellular);
TransportDirections.DefaultDirectionFor(TransportType.Efflux, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.EffluxMucosaIntracellularToLumen);
}
public void should_return_the_expected_direction_for_brain()
{
_transporterExpressionContainer.WithParentContainer(_brain_pls);
TransportDirections.DefaultDirectionFor(TransportType.Influx, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.InfluxBrainPlasmaToInterstitial);
TransportDirections.DefaultDirectionFor(TransportType.BiDirectional, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.BiDirectionalBrainPlasmaInterstitial);
TransportDirections.DefaultDirectionFor(TransportType.Efflux, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.EffluxBrainInterstitialToPlasma);
_transporterExpressionContainer.WithParentContainer(_brain_cell);
TransportDirections.DefaultDirectionFor(TransportType.Influx, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.InfluxBrainInterstitialToTissue);
TransportDirections.DefaultDirectionFor(TransportType.BiDirectional, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.BiDirectionalBrainInterstitialTissue);
TransportDirections.DefaultDirectionFor(TransportType.Efflux, _transporterExpressionContainer)
.ShouldBeEqualTo(TransportDirectionId.EffluxBrainTissueToInterstitial);
}
public void should_use_the_default_settings_otherwise()
{
_transporterWithoutTemplate.TransportDirection.ShouldBeEqualTo(TransportDirections.DefaultDirectionFor(TransportType.Influx, _transporterWithoutTemplate));
}
public void should_use_the_template_defined_in_the_database_if_available()
{
_transporterWithTemplate.TransportDirection.ShouldBeEqualTo(TransportDirections.DefaultDirectionFor(TransportType.Influx, _transporterWithTemplate));
}
public override async Task <MoleculeExpressionContainer> MapToModel(ExpressionContainer snapshot, ExpressionContainerMapperContext snapshotContext)
{
if (snapshot == null)
{
return(null);
}
var molecule = snapshotContext.Molecule;
var expressionParameterCache = snapshotContext.ExpressionParameters;
var expressionContainerParameters = snapshotContext.MoleculeExpressionContainers;
//Value was only defined for older version of the snapshot
if (snapshot.Value.HasValue)
{
var relExp = expressionParameterCache[snapshot.Name];
if (relExp == null)
{
_logger.AddWarning(PKSimConstants.Error.RelativeExpressionContainerNotFound(snapshot.Name));
return(null);
}
await _parameterMapper.MapToModel(snapshot, new ParameterSnapshotContext(relExp, snapshotContext));
}
//We do not return anything as container are created at construction time
if (!(molecule is IndividualTransporter transporter))
{
return(null);
}
var expressionsContainers = expressionContainerParameters.OfType <TransporterExpressionContainer>()
.Where(queryPredicate(snapshotContext.IsV9FormatOrEarlier, snapshot))
.Where(x => x.TransportDirection != TransportDirectionId.None)
.ToList();
if (expressionsContainers.Count == 0)
{
_logger.AddWarning(PKSimConstants.Error.RelativeExpressionContainerNotFound(snapshot.Name));
return(null);
}
var firstExpressionContainer = expressionsContainers[0];
//This is the new format
if (!snapshotContext.IsV9FormatOrEarlier)
{
//we should only have one
firstExpressionContainer.TransportDirection = snapshot.TransportDirection.Value;
return(firstExpressionContainer);
}
expressionsContainers.Each(x => x.TransportDirection = TransportDirections.DefaultDirectionFor(transporter.TransportType, x));
//only one direction to take into consideration. all good, nothing else to do
if (expressionsContainers.Count == 1)
{
return(firstExpressionContainer);
}
//This is the old format. Basolateral was the default
var membraneLocation = ModelValueFor(snapshot.MembraneLocation, MembraneLocation.Basolateral);
MembraneLocationConverter.ConvertMembraneLocationToParameterFraction(expressionsContainers, membraneLocation);
return(firstExpressionContainer);
}
