private TInteractionProcess createInteractionProcess <TInteractionProcess>(FlatProcess flatProcess) where TInteractionProcess : InteractionProcess
{
var interactionProcess = createProcessBaseOn <TInteractionProcess>(flatProcess);
interactionProcess.InteractionType = mapInteractionTypeFrom(flatProcess);
return(interactionProcess);
}
public CompoundProcess MapFrom(FlatProcess flatProcess)
{
if (!flatProcess.IsTemplate)
{
throw new ArgumentException(PKSimConstants.Error.CompoundProcessDeclaredAsNotTemplate(flatProcess.Name));
}
if (flatProcess.GroupName == CoreConstants.Groups.ENZYMATIC_STABILITY_INTRINSIC)
{
return(createProcessBaseOn <EnzymaticProcessWithSpecies>(flatProcess));
}
if (flatProcess.GroupName == CoreConstants.Groups.ENZYMATIC_STABILITY_PARTIAL)
{
return(createProcessBaseOn <EnzymaticProcess>(flatProcess));
}
if (flatProcess.GroupName == CoreConstants.Groups.SPECIFIC_BINDING)
{
return(createProcessBaseOn <SpecificBindingPartialProcess>(flatProcess));
}
if (flatProcess.GroupName == CoreConstants.Groups.ACTIVE_TRANSPORT_INTRINSIC)
{
return(createProcessBaseOn <TransportPartialProcessWithSpecies>(flatProcess));
}
if (flatProcess.GroupName == CoreConstants.Groups.ACTIVE_TRANSPORT)
{
return(createProcessBaseOn <TransportPartialProcess>(flatProcess));
}
if (flatProcess.GroupName == CoreConstants.Groups.IN_VITRO_PROCESSES_ENZYMATIC_STABILITY)
{
return(createProcessBaseOn <EnzymaticProcessWithSpecies>(flatProcess));
}
if (flatProcess.GroupName == CoreConstants.Groups.INHIBITION_PROCESSES)
{
return(createInteractionProcess <InhibitionProcess>(flatProcess));
}
if (flatProcess.GroupName == CoreConstants.Groups.INDUCTION_PROCESSES)
{
return(createInteractionProcess <InductionProcess>(flatProcess));
}
if (flatProcess.GroupName == CoreConstants.Groups.IN_VITRO_PROCESSES_TOTAL_HEPATIC)
{
return(createSystemicProcess(flatProcess, SystemicProcessTypes.Hepatic));
}
if (flatProcess.GroupName == CoreConstants.Groups.SYSTEMIC_PROCESSES)
{
return(createSystemicProcess(flatProcess, typeFrom(flatProcess)));
}
throw new ArgumentException($"Group '{flatProcess.GroupName}' unknown for compound");
}
private SystemicProcess createSystemicProcess(FlatProcess flatProcess, SystemicProcessType processType)
{
var systemicProcess = createProcessBaseOn <SystemicProcess>(flatProcess);
systemicProcess.SystemicProcessType = processType;
systemicProcess.Icon = processType.IconName;
setDefaultSpeciesForProcess(systemicProcess);
return(systemicProcess);
}
private TProcess createProcessBaseOn <TProcess>(FlatProcess flatProcess) where TProcess : CompoundProcess
{
var newProcess = _entityBaseFactory.Create <TProcess>();
var repInfo = _representationInfoRepository.InfoFor(RepresentationObjectType.PROCESS, flatProcess.Name);
newProcess.Name = flatProcess.Name;
newProcess.InternalName = flatProcess.Name;
newProcess.Description = repInfo.Description;
newProcess.Icon = repInfo.IconName;
setDefaultSpeciesForProcess(newProcess as ISpeciesDependentCompoundProcess);
return(newProcess);
}
public PKSimTransport MapFrom(FlatProcess flatProcess)
{
var transport = _entityBaseFactory.Create <PKSimTransport>()
.WithName(flatProcess.Name)
.WithDimension(_dimensionRepository.AmountPerTime);
_parameterContainerTask.AddProcessBuilderParametersTo(transport);
addDescriptorConditions(transport.SourceCriteria, ProcessTagType.Source, transport.Name);
addDescriptorConditions(transport.TargetCriteria, ProcessTagType.Target, transport.Name);
transport.CalculationMethod = flatProcess.CalculationMethod;
transport.Rate = flatProcess.Rate;
transport.Formula = _formulaFactory.RateFor(transport, new FormulaCache());
transport.CreateProcessRateParameter = flatProcess.CreateProcessRateParameter;
return(transport);
}
private IPKSimProcess createProcessFrom(FlatProcess flatProcess)
{
switch (flatProcess.ActionType)
{
case ProcessActionType.Reaction:
var reaction = newReaction();
addReactionPartnersTo(reaction, flatProcess.Name);
return(reaction);
case ProcessActionType.Transport:
return(_entityBaseFactory.Create <PKSimTransport>());
case ProcessActionType.Interaction:
return(interactionProcessFor(flatProcess));
default:
throw new ArgumentOutOfRangeException(flatProcess.ActionType.ToString());
}
}
public IPKSimProcess MapFrom(FlatProcess flatProcess)
{
var activeProcess = createProcessFrom(flatProcess);
if (activeProcess == null)
{
return(null);
}
activeProcess.Name = flatProcess.Name;
activeProcess.CalculationMethod = flatProcess.CalculationMethod;
activeProcess.Rate = flatProcess.Rate;
activeProcess.Formula = _formulaFactory.RateFor(activeProcess.CalculationMethod, activeProcess.Rate, new FormulaCache());
var repInfo = _representationInfoRepository.InfoFor(RepresentationObjectType.PROCESS, activeProcess.Name);
activeProcess.Icon = repInfo.IconName;
updateTransporterDescriptors(activeProcess as PKSimTransport);
activeProcess.CreateProcessRateParameter = flatProcess.CreateProcessRateParameter;
activeProcess.Dimension = activeProcess.Formula.Dimension;
return(activeProcess);
}
private SystemicProcessType typeFrom(FlatProcess flatProcess)
{
if (flatProcess.ProcessType == CoreConstants.ProcessType.ELIMINATION_GFR)
{
return(SystemicProcessTypes.GFR);
}
if (flatProcess.ProcessType == CoreConstants.ProcessType.ELIMINATION)
{
return(SystemicProcessTypes.Renal);
}
if (flatProcess.ProcessType == CoreConstants.ProcessType.SECRETION)
{
return(SystemicProcessTypes.Biliary);
}
if (flatProcess.ProcessType == CoreConstants.ProcessType.METABOLIZATION)
{
return(SystemicProcessTypes.Hepatic);
}
throw new ArgumentException($"Systemic process type for process '{flatProcess.Name}' of type '{flatProcess.ProcessType}' unknown.");
}
private bool processIsNonTemplateReaction(FlatProcess flatProcess)
{
return(!flatProcess.IsTemplate && flatProcess.ActionType == ProcessActionType.Reaction);
}
private InteractionType mapInteractionTypeFrom(FlatProcess flatProcess)
{
return(EnumHelper.ParseValue <InteractionType>(flatProcess.ProcessType));
}
private bool processIsSimulationActiveProcess(FlatProcess process)
{
return(process.IsTemplate && CoreConstants.Groups.AllSimulationActiveProcesses.Contains(process.GroupName));
}
private IPKSimProcess interactionProcessFor(FlatProcess flatInteractionProcess)
{
var interactionType = EnumHelper.ParseValue <InteractionType>(flatInteractionProcess.ProcessType);
return(interactionType.Is(InteractionType.ReactionInducer) ? newReaction() : null);
}
private bool processIsApplication(FlatProcess process)
{
return(process.ProcessType == CoreConstants.ProcessType.APPLICATION);
}
private bool processIsPassiveTransport(FlatProcess process)
{
return((process.ProcessType == CoreConstants.ProcessType.PASSIVE) &&
process.ActionType.Equals(ProcessActionType.Transport));
}
