public void should_have_converted_the_transporter_as_expected()
{
var influx = _individual.MoleculeByName <IndividualTransporter>("T1_Influx");
influx.TransportType.ShouldBeEqualTo(TransportType.Influx);
//checking that it is not set to the default Efflux and that a conversion occurred
var allTransporterContainers = _individual.AllMoleculeContainersFor <TransporterExpressionContainer>(influx);
allTransporterContainers.Any(x => x.TransportDirection.ToString().Contains("Efflux")).ShouldBeFalse();
var efflux_apical_bbb = _individual.MoleculeByName <IndividualTransporter>("T4_Efflux_Apical_BBB");
efflux_apical_bbb.TransportType.ShouldBeEqualTo(TransportType.Efflux);
}
private IReadOnlyCollection <InducedProcess> allInducedProcessesFor(IndividualTransporter transporter, Individual individual)
{
var inducedProcessCache = new Cache <string, InducedProcess>(x => x.Name, x => null);
var allTransporterContainers = individual.AllMoleculeContainersFor <TransporterExpressionContainer>(transporter)
.Where(x => x.TransportDirection != TransportDirectionId.None).ToList();
//Global containers surrogate do not have a logical container associated
var allOrganNames = new HashSet <string>(allTransporterContainers.Select(x => x.LogicalContainerName).Where(x => !string.IsNullOrEmpty(x)));
foreach (var transporterContainer in allTransporterContainers)
{
//Logical containerName is empty for surrogate containers
var logicalContainer = transporterContainer.LogicalContainerName;
var allTransportTemplates = _transportTemplateRepository.All()
.Where(x => x.TransportDirection == transporterContainer.TransportDirection);
//a logical container is defined. We are dealing with a localized transporter
if (!string.IsNullOrEmpty(logicalContainer))
{
//For apical transport for Lumen => Mucosa, the compartment is the name of our mapping
allTransportTemplates = allTransportTemplates
.Where(x => (x.SourceOrgan == logicalContainer || x.SourceCompartment == logicalContainer));
}
foreach (var transportTemplate in allTransportTemplates)
{
var inducedProcess = inducedProcessCache[transportTemplate.ProcessName];
if (inducedProcess == null)
{
inducedProcess = new InducedProcess {
Name = transportTemplate.ProcessName
};
inducedProcess.AddOrgansToExclude(allOrganNames);
inducedProcessCache.Add(inducedProcess);
}
// For lumen transport. The source organ or target organ is in fact defined as a compartment
inducedProcess.AddSourceOrgan(transportTemplate.SourceOrgan.IsLumen() ? transportTemplate.SourceCompartment : transportTemplate.SourceOrgan);
inducedProcess.AddTargetOrgan(transportTemplate.TargetOrgan.IsLumen() ? transportTemplate.TargetCompartment : transportTemplate.TargetOrgan);
}
}
return(inducedProcessCache);
}
private PathCache <TransporterExpressionContainer> allTransporterExpressionContainerFor(Individual individual, IndividualMolecule molecule)
{
var allTransporterExpressionContainer = individual.AllMoleculeContainersFor <TransporterExpressionContainer>(molecule);
return(_containerTask.PathCacheFor(allTransporterExpressionContainer));
}