protected override void DoStart()
{
foreach (var flatStartFormula in _flatMoleculeStartFormulasRepository.All())
{
var moleculePath = _flatContainerRepository.ContainerPathFrom(flatStartFormula.Id);
moleculePath.Add(flatStartFormula.MoleculeName);
var startFormula = new MoleculeStartFormula(moleculePath, flatStartFormula.CalculationMethod,
flatStartFormula.Rate);
_moleculeStartFormulas.Add(startFormula);
}
}
protected override void DoStart()
{
foreach (var flatParameterMapping in _flatParameterMappingRepo.All())
{
ICompoundProcessParameterMapping mapping = new CompoundProcessParameterMapping();
mapping.ProcessName = flatParameterMapping.ProcessName;
mapping.ParameterName = flatParameterMapping.ParameterName;
mapping.MappedParameterPath = _flatContainerRepo.ContainerPathFrom(flatParameterMapping.ContainerId);
mapping.MappedParameterPath.Add(flatParameterMapping.ContainerParameterName);
_parameterMappings.Add(mapping);
}
}
private IContainer neighborFrom(int neighborId, Organism organism)
{
var containerPath = _flatContainerRepository.ContainerPathFrom(neighborId);
//path from the database do not start with root
//if called for individual neighborhood (organism is NOT top container),
//add ROOT as top path entry
if (organism.ParentContainer != null)
{
containerPath.AddAtFront(Constants.ROOT);
}
return(containerPath.Resolve <IContainer>(organism));
}
protected override void DoStart()
{
_parameterMetaDataList = _flatParameterMetaDataRepository.All().ToList();
foreach (var parameterMetaData in _parameterMetaDataList)
{
parameterMetaData.ParentContainerPath = _flatContainerRepository.ContainerPathFrom(parameterMetaData.ContainerId).ToString();
}
//now cache the _parameter values
foreach (var parameterValueMetaDataGroup in _parameterMetaDataList.GroupBy(x => x.ParentContainerPath))
{
_parameterMetaDataCache.Add(parameterValueMetaDataGroup.Key, new List <TParameterMetaData>(parameterValueMetaDataGroup));
}
}
protected override void DoStart()
{
_parameterMetaDataList = _flatParameterMetaDataRepository.All().ToList();
_parameterMetaDataList.Each(parameterMetaData =>
{
parameterMetaData.ParentContainerPath = _flatContainerRepository.ContainerPathFrom(parameterMetaData.ContainerId).ToString();
//Use clone here to ensure that we are not modifying the reference stored in the repository
var valueOrigin = _valueOriginRepository.FindBy(parameterMetaData.ValueOriginId).Clone();
parameterMetaData.ValueOrigin = valueOrigin;
});
//now cache the parameter meta data by container path
foreach (var parameterValueMetaDataGroup in _parameterMetaDataList.GroupBy(x => x.ParentContainerPath))
{
_parameterMetaDataCacheByContainer.Add(parameterValueMetaDataGroup.Key, new List<TParameterMetaData>(parameterValueMetaDataGroup));
}
}
public IObjectPath MapFrom(FlatObjectPath flatObjectPath)
{
IObjectPath objectPath;
if (flatObjectPath.IsAbsolutePath)
{
objectPath = _flatContainerRepository.ContainerPathFrom(flatObjectPath.ContainerId);
}
else
{
objectPath = _relativeObjectPathMapper.MapFrom(flatObjectPath.RelativeObjectPathId);
}
//for molecule amounts, object name used is just a dummy in the database,
//so omit it
if (!flatObjectPath.UseAmount)
{
objectPath.Add(adjustRateObjectName(flatObjectPath.RateObjectName));
}
return(objectPath);
}
public IEnumerable <IContainer> SubContainersFor(Species species, ModelConfiguration modelConfiguration, IContainer parentContainer)
{
IList <IContainer> allSubContainers = new List <IContainer>();
string pathToParentContainer = _entityPathResolver.PathFor(parentContainer);
var flatParentContainer = _flatContainerRepo.ContainerFrom(pathToParentContainer);
var flatModelSubContainers = _modelContainerRepo.AllSubContainerFor(modelConfiguration.ModelName, flatParentContainer.Id);
var allSpeciesSubContainer = speciesSubContainers(species.Name, flatParentContainer.Id);
foreach (var flatModelContainer in flatModelSubContainers)
{
// check if container available in species
if (allSpeciesSubContainer.Contains(flatModelContainer.Id))
{
//model subcontainer available in the species structure - add to model subcontainers and continue
allSubContainers.Add(_flatContainerIdToContainerMapper.MapFrom(flatModelContainer));
continue;
}
// model subcontainer NOT available in species structure.
// In this case, action depends on UsageInIndividuum-flag
if (flatModelContainer.UsageInIndividual == CoreConstants.ORM.UsageInIndividualRequired)
{
throw new ArgumentException(PKSimConstants.Error.ModelContainerNotAvailable(_flatContainerRepo.ContainerPathFrom(flatModelContainer.Id).ToString()));
}
if (flatModelContainer.UsageInIndividual == CoreConstants.ORM.UsageInIndividualOptional)
{
continue;
}
if (flatModelContainer.UsageInIndividual == CoreConstants.ORM.UsageInIndividualExtended)
{
allSubContainers.Add(_flatContainerIdToContainerMapper.MapFrom(flatModelContainer));
continue;
}
throw new ArgumentException(PKSimConstants.Error.UnknownUsageInIndividualFlag(flatModelContainer.UsageInIndividual));
}
return(allSubContainers);
}
public IReadOnlyList <IContainer> SubContainersFor(SpeciesPopulation population, ModelConfiguration modelConfiguration, IContainer parentContainer)
{
var allSubContainers = new List <IContainer>();
string pathToParentContainer = _entityPathResolver.PathFor(parentContainer);
var flatParentContainer = _flatContainerRepo.ContainerFrom(pathToParentContainer);
var flatModelSubContainers = _modelContainerRepo.AllSubContainerFor(modelConfiguration.ModelName, flatParentContainer.Id);
var allSpeciesSubContainer = populationSubContainers(population, flatParentContainer);
foreach (var flatModelContainer in flatModelSubContainers)
{
// check if container available in species
if (allSpeciesSubContainer.Contains(flatModelContainer.Id))
{
//model subcontainer available in the species structure - add to model subcontainers and continue
allSubContainers.Add(_flatContainerIdToContainerMapper.MapFrom(flatModelContainer));
continue;
}
// model subcontainer NOT available in species structure.
// In this case, action depends on UsageInIndividuum-flag
if (flatModelContainer.UsageInIndividual == CoreConstants.ORM.USAGE_IN_INDIVIDUAL_REQUIRED)
{
throw new ArgumentException(PKSimConstants.Error.ModelContainerNotAvailable(_flatContainerRepo.ContainerPathFrom(flatModelContainer.Id).ToString()));
}
if (flatModelContainer.UsageInIndividual == CoreConstants.ORM.USAGE_IN_INDIVIDUAL_OPTIONAL)
{
continue;
}
if (flatModelContainer.UsageInIndividual == CoreConstants.ORM.USAGE_IN_INDIVIDUAL_EXTENDED)
{
allSubContainers.Add(_flatContainerIdToContainerMapper.MapFrom(flatModelContainer));
continue;
}
throw new ArgumentException(PKSimConstants.Error.UnknownUsageInIndividualFlag(flatModelContainer.UsageInIndividual));
}
return(allSubContainers);
}