private void updateTransporterTagsFor(ITransportBuilder transporterBuilder, InducedProcess inducedProcess)
{
var sourceCriteria = transporterBuilder.SourceCriteria;
var allSourceTags = sourceCriteria.OfType <MatchTagCondition>().Select(x => x.Tag).ToList();
var(sourceIsLumen, sourceIsMucosa) = (allSourceTags.Contains(LUMEN), allSourceTags.Contains(MUCOSA));
var targetCriteria = transporterBuilder.TargetCriteria;
var allTargetTags = targetCriteria.OfType <MatchTagCondition>().Select(x => x.Tag).ToList();
var(targetIsLumen, targetIsMucosa) = (allTargetTags.Contains(LUMEN), allTargetTags.Contains(MUCOSA));
var isLumen = sourceIsLumen || targetIsLumen;
var isMucosa = sourceIsMucosa || targetIsMucosa;
if (isLumen && isMucosa)
{
//We just want to remove GI segments from the include list as we know, that the transport is between Lumen and Mucosa in this case
var segmentToDeletes = inducedProcess.OrgansToExclude.Intersect(LumenSegmentsDuodenumToRectum).ToList();
var criteria = sourceIsLumen ? sourceCriteria : targetCriteria;
addAsNotMatchToCriteria(criteria, segmentToDeletes);
return;
}
// This is a specific transport and we do not need to do anything
if (allSourceTags.Count > 1)
{
return;
}
addAsNotMatchToCriteria(sourceCriteria, inducedProcess.OrgansToExclude);
}
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 ITransportBuilder activeTransportFrom(CompoundProcess process, InducedProcess inducedProcess, IFormulaCache formulaCache)
{
//retrieve process for the simulation and create a clone
var simulationProcess = _simulationActiveProcessRepository.TransportFor(inducedProcess.Name, process.InternalName);
if (simulationProcess == null)
{
throw new PKSimException(PKSimConstants.Error.CannotCreateTransportProcessWithKinetic(inducedProcess.Name, process.Name));
}
var activeTransport = _cloner.Clone(simulationProcess);
updateTransporterFormulaFromCache(activeTransport, formulaCache);
//remove all parameters defined in the builder
var allParameters = activeTransport.Parameters.ToList();
allParameters.Each(activeTransport.RemoveParameter);
return(activeTransport);
}
